Contacts of the helix formed by residues 123 - 143 (chain B) in PDB entry 2PEG
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 123 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG* 3.5 6.6 + - - +
120B HIS 3.6 17.0 - - - +
121B ALA* 2.9 11.4 + - - +
122B PHE* 1.3 76.4 - - - +
124B ALA* 1.3 59.8 + - - +
125B GLU* 3.6 8.7 + - - +
126B THR* 2.9 26.1 + - - +
127B GLN 2.8 25.3 + - - -
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Residues in contact with ALA 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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30A SER* 4.6 2.0 - - - +
31A ARG* 3.7 36.5 - - + +
34A VAL* 3.8 30.6 - - + +
35A VAL* 3.4 9.2 - - + +
51A PRO* 5.1 6.7 - - + -
123B THR* 1.3 73.8 - - - +
125B GLU* 1.3 58.6 + - - +
127B GLN* 3.2 2.3 + - - -
128B GLY* 2.8 26.3 + - - -
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 4.5 8.5 - - + +
6B LYS* 2.8 50.1 + - - +
10B ILE* 3.7 12.7 - - + +
123B THR* 3.2 9.0 + - - +
124B ALA* 1.3 79.6 - - - +
126B THR* 1.3 61.9 + - - +
128B GLY* 3.5 1.0 + - - -
129B ALA* 3.2 23.0 + - - +
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Residues in contact with THR 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 4.1 16.8 - - + +
14B ILE* 3.5 30.7 - - + -
118B MET* 4.3 10.3 - - + +
121B ALA 3.7 7.6 + - - +
122B PHE* 3.7 17.9 - - + -
123B THR* 2.9 27.5 + - - +
125B GLU* 1.3 75.5 - - - +
127B GLN* 1.3 66.3 + - - +
129B ALA* 3.3 1.9 + - - +
130B PHE* 2.9 23.9 + - - +
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Residues in contact with GLN 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG* 3.0 35.9 + - - +
35A VAL* 4.0 11.3 - - + +
36A TYR* 4.4 2.2 + - - -
104A HIS* 4.1 6.3 - - - -
105A CYS* 4.4 11.1 - - - -
108A VAL* 3.9 21.6 - - - +
122B PHE* 3.5 29.1 - - + -
123B THR 2.8 13.6 + - - +
124B ALA* 3.6 3.1 - - - +
126B THR* 1.3 78.4 - - - +
128B GLY* 1.3 57.4 + - - +
130B PHE* 4.5 0.2 - - - -
131B GLN* 2.8 65.7 + - + +
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Residues in contact with GLY 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A VAL* 6.1 0.4 - - - -
35A VAL* 3.6 23.5 - - - +
7B GLU* 5.9 0.4 - - - -
124B ALA 2.8 15.3 + - - -
125B GLU* 3.5 2.7 + - - -
127B GLN* 1.3 78.0 - - - +
129B ALA* 1.3 55.4 + - - +
131B GLN* 4.0 1.1 - - - +
132B LYS* 3.0 30.8 + - - +
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B TRP* 5.6 0.2 - - - -
7B GLU* 4.3 22.9 - - + -
10B ILE* 3.7 37.2 - - + -
11B ILE* 3.8 15.3 - - + +
125B GLU 3.2 13.5 + - - +
126B THR 3.3 0.2 + - - -
128B GLY* 1.3 75.4 - - - +
130B PHE* 1.3 63.9 + - - +
132B LYS* 3.3 6.5 + - - +
133B PHE* 3.0 24.3 + - - +
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Residues in contact with PHE 130 (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 ILE* 4.8 3.8 - - + +
14B ILE* 3.9 24.6 - - + +
15B PHE* 3.8 32.5 - + - -
18B MET* 4.6 4.0 - - + -
71B LEU* 5.7 0.2 - - + -
110B ILE* 3.7 20.9 - - + -
111B THR* 3.6 28.3 - - + -
114B LEU* 3.6 32.3 - - + -
122B PHE* 4.4 9.4 - + + -
126B THR 2.9 18.6 + - - +
127B GLN 3.8 2.5 - - - +
129B ALA* 1.3 76.7 - - - +
131B GLN* 1.3 63.5 + - - +
133B PHE* 3.2 9.3 + + - +
134B LEU* 3.0 48.5 + - + +
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Residues in contact with GLN 131 (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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35A VAL* 3.5 17.5 - - + +
36A TYR* 2.9 26.0 + - - -
104A HIS* 2.9 20.8 + - - -
108B ASP* 5.7 1.8 - - - +
111B THR* 3.7 21.1 - - + +
127B GLN* 2.8 52.5 + - + +
128B GLY* 4.2 2.2 - - - +
130B PHE* 1.3 75.9 - - + +
132B LYS* 1.3 57.7 + - - +
134B LEU* 3.3 6.9 + - - +
135B ALA* 2.9 29.6 + - - +
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Residues in contact with LYS 132 (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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1B VAL* 2.8 50.5 - - + +
2B GLU 4.3 3.2 + - - -
3B TRP* 3.5 11.4 - - + -
7B GLU* 3.2 31.3 + - - +
128B GLY 3.0 19.8 + - - +
129B ALA* 3.7 5.4 - - - +
130B PHE 3.2 0.4 - - - -
131B GLN* 1.3 77.4 - - - +
133B PHE* 1.3 63.1 + - - +
135B ALA* 3.3 8.1 + - + +
136B VAL* 3.2 23.1 + - + +
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Residues in contact with PHE 133 (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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3B TRP* 3.7 12.4 - + - -
11B ILE* 3.8 22.4 - - + -
15B PHE* 3.9 31.4 - + - -
71B LEU* 3.5 31.4 - - + -
74B GLY* 3.7 20.0 - - - -
75B VAL* 3.6 13.2 - - + -
78B MET* 4.4 9.4 - - + -
81B ILE* 3.8 21.8 - - + -
129B ALA 3.0 12.5 + - - +
130B PHE* 3.6 9.6 - + - +
132B LYS* 1.3 76.1 - - - +
134B LEU* 1.3 71.4 + - + +
136B VAL* 3.3 4.3 + - - +
137B VAL* 3.2 38.9 + - + +
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Residues in contact with LEU 134 (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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71B LEU* 3.9 34.3 - - + -
107B SER* 3.3 37.0 - - - +
110B ILE* 4.3 10.1 - - + -
111B THR* 3.7 11.9 - - - +
130B PHE* 3.0 49.0 + - + +
131B GLN* 3.9 7.4 - - - +
133B PHE* 1.3 87.6 - - + +
135B ALA* 1.3 57.1 + - - +
137B VAL* 3.2 5.3 + - + +
138B VAL* 2.8 34.2 + - + +
400B HEM 6.1 0.9 - - + -
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Residues in contact with ALA 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B SER* 5.0 0.6 - - - -
131B GLN 2.9 17.9 + - - +
132B LYS* 3.4 10.1 - - + +
133B PHE 3.2 0.2 - - - -
134B LEU* 1.3 76.1 - - - +
136B VAL* 1.3 58.9 + - + +
138B VAL* 3.3 8.4 + - - +
139B SER* 2.8 35.9 + - - -
144B GLN* 5.1 0.2 + - - -
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Residues in contact with VAL 136 (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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1B VAL* 3.7 30.5 - - + +
3B TRP* 4.2 9.4 - - + -
81B ILE* 3.5 36.6 - - + -
82B ALA* 5.2 2.9 - - + +
132B LYS* 3.2 15.1 + - + +
133B PHE* 3.3 6.7 + - - +
135B ALA* 1.3 77.2 - - + +
137B VAL* 1.3 63.1 + - - +
139B SER* 3.4 7.8 + - - +
140B ALA* 3.2 21.1 + - - +
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Residues in contact with VAL 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 3.8 22.9 - - + -
81B ILE* 4.0 12.8 - - + -
85B TYR* 3.9 29.8 - - + -
133B PHE* 3.2 40.1 + - + +
134B LEU* 3.2 9.7 + - + +
136B VAL* 1.3 75.9 - - - +
138B VAL* 1.3 59.2 + - + +
140B ALA* 3.1 4.8 + - - +
141B LEU* 2.9 48.2 + - + +
400B HEM 4.5 2.9 - - + -
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Residues in contact with VAL 138 (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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100B PRO 5.4 2.7 - - - +
103B PHE* 3.5 42.0 - - + +
104B LYS* 4.0 20.6 - - + +
107B SER* 3.8 15.5 - - - +
134B LEU* 2.8 20.6 + - + +
135B ALA* 3.6 7.6 - - - +
137B VAL* 1.3 75.2 - - + +
139B SER* 1.3 60.0 + - - +
141B LEU* 3.9 3.9 - - + +
142B GLY* 2.9 28.9 + - - -
144B GLN* 4.1 14.3 + - - +
400B HEM 5.8 3.6 - - + -
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Residues in contact with SER 139 (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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135B ALA* 2.8 21.1 + - - +
136B VAL* 3.6 8.4 - - - +
138B VAL* 1.3 78.1 - - - +
140B ALA* 1.3 61.2 + - - +
143B LYS 3.9 11.4 - - - -
144B GLN* 2.9 42.3 - - - +
146B HIS* 3.8 15.4 + - - -
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Residues in contact with ALA 140 (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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81B ILE 4.0 2.5 - - - +
82B ALA* 3.6 36.1 - - + +
85B TYR* 3.9 17.9 - - + +
86B ALA* 5.5 0.9 - - - -
89B SER* 3.3 16.7 + - - -
136B VAL 3.2 9.2 + - - +
137B VAL* 3.1 10.6 + - - +
139B SER* 1.3 76.7 + - - +
141B LEU* 1.3 64.0 + - - +
143B LYS* 3.4 9.5 + - - +
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Residues in contact with LEU 141 (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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85B TYR* 4.1 14.6 - - + -
88B LEU* 4.0 31.0 - - + +
89B SER* 2.8 34.2 + - - +
92B HIS* 5.0 3.1 - - - +
103B PHE* 3.8 34.3 - - + -
137B VAL* 2.9 30.5 + - + +
138B VAL* 3.9 4.5 - - - +
140B ALA* 1.3 77.5 - - - +
142B GLY* 1.3 59.1 + - - +
143B LYS* 3.1 5.6 - - - +
400B HEM 3.3 44.9 - - + -
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Residues in contact with GLY 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B PRO* 3.9 31.4 - - - +
103B PHE* 3.9 8.4 - - - -
138B VAL 2.9 15.7 + - - -
141B LEU* 1.3 73.1 - - - +
143B LYS* 1.3 78.8 + - - +
144B GLN* 3.5 6.8 - - - +
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Residues in contact with LYS 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B SER* 2.8 37.9 + - - +
90B THR* 4.1 9.9 + - - +
93B SER* 3.0 37.3 + - - -
94B GLU* 5.8 0.6 - - - +
100B PRO* 5.9 1.8 - - + -
139B SER 3.9 1.5 - - - -
140B ALA* 3.4 13.2 + - - +
141B LEU 3.1 4.7 - - - +
142B GLY* 1.3 87.9 - - - +
144B GLN* 1.3 64.5 + - - +
145B TYR* 3.9 11.1 + - - -
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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