Contacts of the helix formed by residues 108 - 121 (chain B) in PDB entry 4L57
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 CYS 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71B PHE* 3.8 27.4 - - + -
101B PRO* 3.8 7.9 - - - -
102B LEU* 3.6 24.7 - - + -
104B LYS 4.2 8.3 - - - +
105B TYR* 3.0 14.3 + - - +
107B HIS* 1.3 79.3 - - - +
109B VAL* 1.3 68.7 + - - +
110B GLY 3.5 1.3 - - - -
111B GLU* 3.3 1.5 + - - +
112B LYS* 3.0 57.8 + - - +
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PRO* 3.6 31.6 - - + -
105B TYR* 3.2 32.6 + - + +
106B HIS 4.7 0.6 + - - +
108B CYS* 1.3 76.8 - - + +
110B GLY* 1.3 62.9 + - - +
112B LYS* 3.4 8.2 + - - +
113B TYR* 3.4 24.8 - - + -
130B LEU* 3.3 28.9 - - + -
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Residues in contact with GLY 110 (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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106B HIS 5.1 4.6 + - - -
108B CYS 4.8 0.4 - - - +
109B VAL* 1.3 78.9 - - - +
111B GLU* 1.3 62.5 + - - +
113B TYR* 3.3 9.2 + - - +
114B ARG* 3.1 22.0 + - - +
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PRO* 3.7 6.4 - - - +
69B GLY* 2.8 31.4 + - - -
70B PHE 3.5 0.3 + - - -
71B PHE* 3.1 19.2 + - + -
72B LEU* 2.9 42.4 + - + +
107B HIS* 3.0 31.8 + - - +
108B CYS 3.3 1.7 + - - +
109B VAL 3.3 0.4 - - - -
110B GLY* 1.3 77.8 - - - +
112B LYS* 1.3 57.4 + - - +
114B ARG* 3.4 6.9 + - - +
115B TRP* 2.8 30.1 + - - +
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Residues in contact with LYS 112 (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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11B MET* 3.6 27.4 - - + +
12B ASP* 2.9 34.1 + - - -
71B PHE* 3.9 15.3 - - + -
99B THR* 2.8 34.2 + - + +
100B SER 3.9 9.6 - - - -
101B PRO* 5.0 2.7 - - + -
108B CYS* 3.0 45.2 + - - +
109B VAL* 3.7 5.6 - - - +
110B GLY 3.3 0.2 - - - -
111B GLU* 1.3 73.9 - - - +
113B TYR* 1.4 69.8 + - + +
115B TRP* 3.3 2.9 + - - +
116B VAL* 3.1 29.0 + - - +
128B ILE* 4.9 1.8 - - + -
130B LEU* 4.7 9.6 - - + -
202B PO4 3.6 0.4 + - - -
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Residues in contact with TYR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B VAL* 3.4 14.4 - - + +
110B GLY* 3.3 10.8 + - - +
112B LYS* 1.4 78.3 - - - +
114B ARG* 1.3 59.6 + - - +
116B VAL* 3.3 4.2 + - - +
117B GLU* 3.0 27.6 + - - +
125B VAL* 3.6 31.3 - - + +
128B ILE* 3.6 41.5 + - + +
130B LEU* 3.6 41.4 + - + +
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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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72B LEU* 3.4 26.4 - - + +
110B GLY 3.1 16.5 + - - +
111B GLU* 3.8 1.3 - - - +
113B TYR* 1.3 73.2 - - - +
115B TRP* 1.3 60.8 + - - +
117B GLU* 3.2 33.1 + - - -
118B GLN* 2.9 59.0 + - - +
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Residues in contact with TRP 115 (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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11B MET* 3.7 25.4 - - + -
15B LEU* 3.5 35.4 - - + -
16B ALA* 3.8 16.8 - - + -
71B PHE 3.4 15.5 - - - +
72B LEU* 3.4 28.9 - - - +
74B LEU* 2.9 23.6 + - + +
76B PRO* 3.9 20.6 - - + -
81B LEU* 4.0 20.2 - - + -
111B GLU 2.8 17.8 + - - +
112B LYS* 3.6 5.8 - - - +
113B TYR 3.3 0.2 - - - -
114B ARG* 1.3 77.4 - - - +
116B VAL* 1.3 64.9 + - + +
118B GLN* 4.8 1.6 - - - -
119B HIS* 2.9 65.0 + + + -
120B LEU* 4.9 4.9 - - + -
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Residues in contact with VAL 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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11B MET* 3.8 21.1 - - + -
15B LEU* 5.9 0.4 - - + -
97B ILE* 4.0 19.7 - - + -
112B LYS 3.1 15.5 + - - +
113B TYR 3.7 6.5 - - - +
115B TRP* 1.3 85.4 - - + +
117B GLU* 1.3 57.8 + - - +
120B LEU* 2.8 31.0 + - + +
121B GLY 3.1 5.0 + - - -
124B PHE* 3.7 40.8 - - + +
125B VAL* 3.7 6.5 - - + +
128B ILE* 3.8 15.7 - - + -
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Residues in contact with GLU 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 TYR 3.0 14.4 + - - +
114B ARG* 3.2 40.3 + - - +
116B VAL* 1.3 75.3 - - - +
118B GLN* 1.3 60.5 + - + +
121B GLY* 3.0 26.7 + - - -
122B PRO* 4.4 23.2 - - + +
125B VAL* 3.5 19.8 - - + +
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Residues in contact with GLN 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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72B LEU* 4.0 22.2 - - - +
114B ARG* 2.9 57.6 + - - +
115B TRP* 4.0 3.7 - - - +
117B GLU* 1.3 80.8 - - + +
119B HIS* 1.3 71.0 + - + +
121B GLY* 4.6 0.9 + - - -
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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
----------------------------------------------------------
72B LEU 4.7 3.6 + - - -
74B LEU 4.2 4.0 + - - -
76B PRO* 3.8 30.6 - - + +
81B LEU* 3.9 26.2 - - + +
115B TRP* 2.9 73.7 + + + +
118B GLN* 1.3 87.7 + - + +
120B LEU* 1.3 65.5 + - - +
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Residues in contact with LEU 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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15B LEU* 4.5 8.7 - - + -
81B LEU* 3.7 46.2 - - + +
84B VAL* 4.5 11.9 - - + -
85B ARG* 4.2 15.8 - - + +
97B ILE* 4.0 26.9 - - + -
115B TRP* 4.9 6.3 - - + -
116B VAL* 2.8 16.2 + - + +
119B HIS* 1.3 76.9 - - + +
121B GLY* 1.3 61.7 + - - +
123B GLN* 4.1 8.3 + - - +
124B PHE* 3.5 42.1 - - + -
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Residues in contact with GLY 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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116B VAL 3.1 2.1 + - - +
117B GLU* 3.0 21.2 + - - -
118B GLN 4.5 0.4 + - - -
119B HIS 3.8 0.6 - - - -
120B LEU* 1.3 78.4 - - - +
122B PRO* 1.4 77.0 - - - +
123B GLN* 3.3 8.1 - - - -
124B PHE* 3.1 13.3 + - - +
125B VAL* 3.5 11.6 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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