Contacts of the helix formed by residues 105 - 127 (chain B) in PDB entry 3ZPL
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B ARG* 3.3 5.2 + - - +
86B GLY 2.7 27.5 + - - +
87B TRP 3.1 6.7 + - - -
88B VAL 3.8 22.4 - - - +
89B ARG* 4.1 22.2 - - + +
103B ILE 3.5 0.4 + - - -
104B LEU* 1.3 77.1 - - - +
106B ASP* 1.3 65.1 + - - +
107B GLU* 3.3 16.0 - - - +
108B GLY 3.0 15.2 + - - -
109B TYR 3.1 17.2 + - - -
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Residues in contact with ASP 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ARG* 3.1 25.8 + - - +
105B THR* 1.3 73.6 - - - +
107B GLU* 1.3 64.9 + - - +
109B TYR* 3.0 8.7 + - - +
110B GLU* 2.9 29.2 + - + +
4E GLU* 5.7 0.5 - - - +
5E PRO* 6.0 0.3 - - - +
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Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ASN 5.4 0.4 - - - +
86B GLY* 3.0 35.1 - - - +
87B TRP* 4.1 7.9 - - + +
105B THR* 3.3 17.3 - - - +
106B ASP* 1.3 83.2 + - - +
108B GLY* 1.3 60.7 + - - +
110B GLU* 3.1 10.4 + - - +
111B VAL* 3.0 25.8 + - - +
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Residues in contact with GLY 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 4.5 0.6 - - - +
87B TRP* 3.7 22.0 - - - -
104B LEU* 3.6 22.7 - - - -
105B THR* 3.0 14.5 + - - -
107B GLU* 1.3 74.8 - - - +
109B TYR* 1.3 63.7 + - - +
111B VAL* 3.1 13.3 + - - +
112B LEU* 3.1 18.8 + - - +
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Residues in contact with TYR 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ALA* 4.4 6.7 - - + -
57B ARG* 4.0 18.8 - - - +
104B LEU* 3.7 22.4 - - + +
105B THR 3.1 11.7 + - - +
106B ASP* 3.0 10.8 + - - +
108B GLY* 1.3 74.4 - - - +
110B GLU* 1.3 61.9 + - + +
112B LEU* 3.3 7.1 + - + +
113B ARG* 3.1 37.5 + - + +
5E PRO* 3.5 36.0 + - + +
6E ARG 3.0 20.1 + - - -
7E TRP* 3.3 32.7 + + - -
117F PRO* 6.0 2.3 - - - +
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Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ASP* 2.9 14.0 + - + +
107B GLU* 3.1 14.5 + - - +
109B TYR* 1.3 77.6 - - + +
111B VAL* 1.3 59.9 + - - +
113B ARG* 2.7 45.5 + - - +
114B ARG* 3.0 30.7 + - - +
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ALA* 4.5 11.2 - - - +
40B MET* 4.2 24.0 - - + -
48B LEU* 5.2 0.7 - - + -
87B TRP* 3.4 39.7 - - + +
107B GLU* 3.0 10.5 + - + +
108B GLY* 3.1 8.0 + - - +
110B GLU* 1.3 73.9 - - - +
112B LEU* 1.3 57.8 + - + +
114B ARG* 4.4 4.5 - - - -
115B THR* 2.6 50.4 + - + +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B TYR* 4.8 9.9 - - + +
48B LEU* 3.6 44.4 - - + +
49B VAL* 4.0 7.9 - - + -
52B ALA* 3.6 31.9 - - + -
104B LEU* 4.7 3.1 - - + -
108B GLY 3.1 18.8 + - - +
109B TYR* 3.6 8.5 - - + +
110B GLU 3.3 0.2 - - - -
111B VAL* 1.3 77.4 - - + +
113B ARG* 1.3 61.4 + - - +
115B THR* 3.1 5.3 + - - -
116B ALA* 2.8 36.6 + - - +
7E TRP* 3.8 30.5 - - + +
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Residues in contact with ARG 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B TYR* 3.1 27.6 + - + +
110B GLU* 2.7 43.9 + - - +
111B VAL 3.4 0.2 - - - -
112B LEU* 1.3 78.3 - - - +
114B ARG* 1.3 66.7 + - - +
116B ALA* 5.3 1.1 - - - -
117B PRO* 3.7 16.2 - - - +
7E TRP* 5.1 4.7 - - - +
113F ARG* 4.8 13.3 - - - +
117F PRO* 5.9 7.6 - - + -
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Residues in contact with ARG 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B GLU* 3.0 21.6 + - - +
111B VAL* 3.9 6.7 - - - +
112B LEU 3.2 0.2 - - - -
113B ARG* 1.3 82.1 - - - +
115B THR* 1.3 66.3 + - + +
117B PRO* 4.2 8.0 - - - +
118B GLY 5.3 0.5 + - - -
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Residues in contact with THR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLN* 4.9 1.7 + - - -
34B LEU* 5.2 3.1 - - - -
37B ASP* 3.5 18.6 - - + +
38B ALA* 3.4 31.4 - - + +
45B TYR* 3.3 22.6 - - - -
111B VAL* 2.6 28.0 + - + +
112B LEU 3.6 0.5 + - - -
114B ARG* 1.3 84.0 - - + +
116B ALA* 1.3 69.8 + - - +
117B PRO* 3.3 2.7 - - - -
118B GLY* 2.9 16.0 + - - +
119B HIS* 3.1 10.0 + - - +
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Residues in contact with ALA 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B TYR* 3.0 21.3 - - - +
112B LEU 2.8 21.2 + - - +
113B ARG* 5.3 0.7 - - - -
115B THR* 1.3 73.0 + - - +
117B PRO* 1.4 61.3 - - + +
119B HIS* 2.9 2.5 + - - +
120B VAL* 2.6 46.9 + - + +
7E TRP* 4.2 20.2 - - + -
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Residues in contact with PRO 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ARG 3.7 17.5 - - - +
114B ARG 4.2 7.4 - - - +
115B THR 3.6 1.3 - - - -
116B ALA* 1.4 93.8 - - + +
118B GLY* 1.3 63.7 + - - +
120B VAL* 3.8 7.0 - - + +
121B ASP* 3.0 31.7 + - - +
113F ARG* 6.1 5.4 - - + -
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Residues in contact with GLY 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B GLN* 3.7 10.8 + - - +
37B ASP* 5.3 4.0 - - - -
114B ARG 5.3 0.6 + - - -
115B THR 2.9 14.8 + - - -
117B PRO* 1.3 73.9 - - - +
119B HIS* 1.3 61.8 + - - -
121B ASP* 3.1 11.8 + - - +
122B ALA* 3.0 21.5 + - - +
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Residues in contact with HIS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A TRP* 4.5 7.2 + - - -
30B LEU* 4.3 8.9 - - + +
33B GLN* 3.2 27.0 + - - +
34B LEU* 3.4 32.6 - - + +
42B HIS* 3.7 22.8 + + - -
45B TYR* 3.7 33.0 - + - +
115B THR 3.1 6.2 + - - +
116B ALA 2.9 7.4 + - - +
118B GLY* 1.3 74.4 - - - +
120B VAL* 1.3 68.3 + - + +
122B ALA* 3.5 1.7 + - - +
123B VAL* 3.1 47.8 + - + +
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ARG 4.7 12.3 - - - +
7A TRP* 5.3 0.7 - - - -
8A LEU* 3.9 36.3 - - + +
116B ALA* 2.6 32.3 + - + +
117B PRO* 3.8 6.5 - - + +
119B HIS* 1.3 75.9 - - + +
121B ASP* 1.3 55.8 + - - +
123B VAL* 3.1 7.8 + - - +
124B ARG* 2.8 36.5 + - + +
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Residues in contact with ASP 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PRO* 4.5 15.6 - - - +
6A ARG 5.0 3.5 - - - +
117B PRO* 3.0 20.6 + - - +
118B GLY* 3.3 11.1 - - - +
120B VAL* 1.3 73.7 - - - +
122B ALA* 1.3 55.5 + - - +
124B ARG* 2.9 29.6 + - - +
125B GLN* 2.7 49.6 + - - +
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B HIS* 4.3 14.6 + - + +
30B LEU* 4.1 14.5 - - + +
33B GLN* 3.9 28.3 - - + +
118B GLY 3.0 9.8 + - - +
119B HIS 3.7 7.4 - - - +
120B VAL 3.3 0.2 - - - -
121B ASP* 1.3 78.6 - - - +
123B VAL* 1.3 57.4 + - - +
125B GLN* 4.2 7.3 - - - +
126B ALA* 3.2 30.8 + - - +
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 4.9 7.6 - - + -
16A TRP* 3.7 50.9 - - + +
26B LEU* 5.9 0.2 - - - -
30B LEU* 4.0 9.6 - - + -
119B HIS* 3.1 46.1 + - + +
120B VAL* 3.6 6.1 - - - +
122B ALA* 1.3 73.9 - - - +
124B ARG* 1.3 65.0 + - - +
126B ALA* 4.8 2.0 - - - -
127B VAL* 3.3 23.8 + - - +
128B PHE* 3.8 14.0 + - + -
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Residues in contact with ARG 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PRO* 3.8 25.8 - - - +
6A ARG* 3.4 43.9 - - - +
8A LEU* 3.3 28.3 - - + -
120B VAL* 2.8 17.5 + - - +
121B ASP* 2.9 47.4 + - - +
123B VAL* 1.3 73.2 - - - +
125B GLN* 1.3 80.0 + - - +
127B VAL 3.1 0.3 + - - -
128B PHE* 3.0 29.3 + - + +
129B ASP* 2.7 42.1 + - - +
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Residues in contact with GLN 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B HIS* 6.3 1.3 - - - +
121B ASP* 2.7 33.6 + - - +
122B ALA* 4.3 5.9 + - - +
124B ARG* 1.3 96.8 - - - +
126B ALA* 1.3 59.5 + - - +
129B ASP* 4.0 9.7 - - - +
130B ARG* 3.1 30.6 + - - +
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A VAL* 4.1 17.8 - - - +
150A LEU* 4.5 11.2 - - + -
26B LEU* 3.9 27.6 - - + -
29B HIS* 4.3 13.7 + - + +
122B ALA 3.2 19.3 + - - +
123B VAL* 4.4 0.7 - - - +
125B GLN* 1.3 78.6 - - - +
127B VAL* 1.3 61.4 + - + +
130B ARG* 3.7 22.5 + - - +
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A TRP* 4.2 15.0 - - + -
146A VAL* 4.5 13.0 - - + -
26B LEU* 4.0 28.7 - - + -
123B VAL 3.3 13.3 + - - +
124B ARG 3.1 5.7 + - - -
126B ALA* 1.3 87.3 - - + +
128B PHE* 1.3 81.5 + - + +
129B ASP 3.4 0.4 - - - -
130B ARG* 2.9 26.3 + - - +
131B LEU* 3.5 29.3 - - + +
139B LEU* 4.6 11.0 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il