Contacts of the helix formed by residues 81 - 95 (chain B) in PDB entry 4P22
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 ARG 81 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B GLY 3.4 2.8 + - - -
80B LEU* 1.3 84.1 - - - +
82B GLY* 1.3 68.7 + - - +
83B LEU* 3.3 4.3 - - + +
84B GLY 3.0 11.5 + - - +
85B VAL* 3.0 6.2 + - - +
110B ALA* 3.5 26.1 + - - +
111B ASP* 2.8 32.9 + - + +
115B GLN* 3.7 6.7 - - - -
127B ARG* 3.8 20.4 - - - +
165B THR* 5.5 1.1 - - - +
166B ASN* 3.1 45.3 + - + +
393B ASP* 3.6 29.8 + - - +
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Residues in contact with GLY 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ARG* 1.3 76.0 - - - +
83B LEU* 1.3 61.4 + - - +
85B VAL* 3.1 4.0 - - - +
86B GLU* 2.9 29.7 + - - +
111B ASP 5.0 0.8 + - - -
114B SER* 3.2 29.4 - - - -
115B GLN* 3.2 21.7 - - - +
393B ASP* 4.8 4.4 + - - -
398B ASN* 4.3 1.5 - - - +
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ARG* 3.3 3.2 - - + +
82B GLY* 1.3 75.5 - - - +
84B GLY* 1.3 62.1 + - - +
86B GLU* 3.3 2.7 + - - +
87B ILE* 3.1 26.4 + - + +
165B THR* 4.2 12.1 - - + -
189B ALA* 3.5 36.1 - - + +
190B ASP* 3.7 19.5 - - - +
191B THR* 4.0 6.1 - - - +
393B ASP* 5.5 0.8 + - - +
398B ASN* 3.5 42.8 - - - +
401B ILE* 3.9 12.6 - - + -
402B GLY* 3.7 17.0 - - - +
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Residues in contact with GLY 84 (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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77B VAL* 3.6 11.8 - - - +
79B GLY 3.3 25.7 + - - -
80B LEU* 4.9 2.2 - - - -
81B ARG* 3.0 5.4 + - - +
83B LEU* 1.3 78.1 - - - +
85B VAL* 1.3 59.2 + - - +
87B ILE* 3.4 1.8 + - - +
88B ALA* 2.9 28.4 + - - +
165B THR* 3.7 16.9 + - - +
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 4.3 5.3 - - + +
81B ARG 3.0 6.5 + - - +
82B GLY* 3.1 18.4 - - - +
84B GLY* 1.3 73.2 - - - +
86B GLU* 1.3 60.8 + - - +
88B ALA* 3.7 6.0 - - - +
89B LYS* 3.0 27.9 + - - +
115B GLN* 3.6 47.1 - - - +
116B PHE* 3.9 15.9 - - + -
117B TYR* 3.5 33.7 - - + -
131B SER* 4.7 1.1 - - - +
135B LEU* 4.3 13.2 - - + +
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Residues in contact with GLU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLU* 4.5 0.2 - - - +
89A LYS* 2.7 35.0 + - - -
90A ASN* 4.3 1.0 - - - +
93A LEU* 5.1 3.6 - - - +
399A ALA* 5.2 0.9 - - - +
82B GLY* 2.9 27.0 + - - +
83B LEU 3.4 5.8 - - - +
84B GLY 3.1 0.2 - - - -
85B VAL* 1.3 75.9 - - - +
87B ILE* 1.3 64.8 + - - +
89B LYS* 3.1 20.4 + - - +
90B ASN* 3.0 34.2 + - - +
114B SER* 5.2 3.3 + - - +
115B GLN 5.8 0.4 + - - +
116B PHE* 3.4 18.5 - - + -
395B ALA* 5.1 2.3 - - - +
398B ASN* 4.0 21.5 - - + +
399B ALA* 4.0 17.9 - - - +
402B GLY* 4.4 4.7 - - - -
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Residues in contact with ILE 87 (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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77B VAL* 4.3 17.0 - - + -
83B LEU* 3.1 17.6 + - + +
84B GLY 3.7 6.3 - - - +
86B GLU* 1.3 79.0 - - - +
88B ALA* 1.3 63.5 + - - +
90B ASN* 3.3 3.8 + - - +
91B ILE* 3.0 24.9 + - + +
163B VAL* 3.9 24.9 - - + -
165B THR* 4.0 15.3 - - + -
189B ALA* 4.1 7.2 - - + -
402B GLY* 3.8 26.5 - - - +
405B ALA* 3.6 22.0 - - + -
406B ALA* 4.6 13.0 - - - +
409B VAL* 4.6 9.9 - - + -
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 4.4 14.8 - - + -
80B LEU* 6.0 0.4 - - + -
84B GLY 2.9 17.5 + - - +
85B VAL* 3.7 6.3 - - - +
86B GLU 3.2 0.2 - - - -
87B ILE* 1.3 77.0 - - - +
89B LYS* 1.3 56.8 + - - +
91B ILE* 3.2 5.3 + - - +
92B ILE* 2.9 39.6 + - + +
99B VAL* 4.9 1.8 - - + -
101B LEU* 4.0 26.9 - - + -
135B LEU* 4.1 11.4 - - + -
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Residues in contact with LYS 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLU* 3.2 28.8 + - - +
89A LYS* 3.5 3.3 - - - +
116A PHE* 4.4 15.9 - - + -
399A ALA* 4.3 0.8 - - - +
85B VAL 3.0 15.6 + - - +
86B GLU* 3.1 28.7 + - - -
88B ALA* 1.3 76.7 - - - +
90B ASN* 1.3 78.6 + - - +
93B LEU* 3.0 45.8 + - + +
116B PHE* 4.0 22.0 - - + -
117B TYR* 4.8 1.3 - - - +
135B LEU* 3.9 7.4 - - + +
138B LEU* 3.4 29.8 - - + +
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Residues in contact with ASN 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLU* 4.3 1.4 - - - +
395A ALA* 3.9 19.6 - - - +
396A PRO* 4.3 6.5 - - + +
399A ALA* 3.3 28.0 - - - +
86B GLU* 3.0 21.2 + - - +
87B ILE 3.6 0.7 - - - +
89B LYS* 1.3 102.2 + - - +
91B ILE* 1.3 58.9 + - - +
93B LEU 3.7 0.2 + - - -
94B GLY* 3.0 20.8 + - - -
402B GLY 3.0 27.9 + - - -
403B GLY* 3.7 2.4 - - - -
406B ALA* 3.5 18.4 - - + -
410B MET* 3.6 8.2 - - - +
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Residues in contact with ILE 91 (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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75B VAL* 5.1 5.2 - - + -
77B VAL* 5.1 6.5 - - + -
87B ILE* 3.0 15.8 + - + +
88B ALA* 3.2 9.4 + - - +
90B ASN* 1.3 74.4 - - - +
92B ILE* 1.3 61.0 + - - +
94B GLY* 3.4 1.6 + - - -
95B GLY 3.1 19.4 + - - -
96B VAL* 3.5 21.8 + - + +
99B VAL* 3.4 29.8 - - + -
406B ALA* 3.3 48.9 - - + +
409B VAL* 3.5 28.9 - - + -
410B MET* 3.6 14.1 - - + -
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Residues in contact with ILE 92 (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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88B ALA 2.9 21.7 + - - +
89B LYS 3.9 3.4 - - - +
91B ILE* 1.3 75.5 - - - +
93B LEU* 1.3 65.6 + - - +
94B GLY 3.0 1.3 - - - -
95B GLY* 3.0 7.3 + - - +
99B VAL* 3.6 25.1 - - + -
135B LEU* 3.9 26.2 - - + +
136B ALA 6.0 0.2 - - - +
138B LEU* 3.9 16.6 - - + -
139B ASN* 2.9 42.2 + - + +
142B VAL* 3.8 14.2 - - + +
144B VAL* 3.5 35.9 - - + -
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Residues in contact with LEU 93 (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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86A GLU* 4.8 2.7 - - - +
112A LEU 5.0 2.5 - - - +
113A SER 3.3 24.1 - - - +
114A SER* 4.2 14.4 - - - +
115A GLN 5.2 0.2 - - - +
116A PHE* 4.3 21.5 - - + -
395A ALA* 3.5 26.9 - - + -
64B HIS* 3.2 14.1 + - - -
67B MET* 3.4 16.3 - - - +
89B LYS* 3.0 41.4 + - + +
90B ASN* 3.9 1.1 - - - +
92B ILE* 1.3 78.1 - - - +
94B GLY* 1.3 60.4 + - - +
95B GLY 3.5 0.5 + - - -
138B LEU* 4.1 28.0 - - + +
139B ASN* 4.1 4.2 + - - +
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Residues in contact with GLY 94 (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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395A ALA* 4.6 0.2 - - - +
64B HIS* 2.7 44.4 + - - +
67B MET* 4.6 4.1 - - - +
71B GLN* 5.7 0.3 + - - -
90B ASN 3.0 9.4 + - - -
91B ILE 3.6 0.9 - - - -
92B ILE 3.0 1.0 - - - -
93B LEU* 1.3 79.0 - - - +
95B GLY* 1.3 61.6 + - - +
96B VAL 3.6 1.6 - - - -
410B MET* 3.4 21.6 - - - +
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Residues in contact with GLY 95 (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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67B MET* 4.3 12.2 - - - +
71B GLN* 3.2 28.2 + - - +
91B ILE 3.1 1.4 + - - -
92B ILE 3.0 15.7 + - - -
93B LEU 3.3 0.2 - - - -
94B GLY* 1.3 81.3 - - - +
96B VAL* 1.3 68.3 + - - +
139B ASN* 3.9 6.7 - - - -
142B VAL* 3.7 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