Contacts of the helix formed by residues 91 - 105 (chain B) in PDB entry 4G1U
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 GLY 91 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B PRO 4.3 1.1 - - - -
88B GLY 4.9 0.7 - - - -
89B LEU 3.1 7.6 - - - +
90B LEU* 1.3 80.6 - - - +
92B ILE* 1.3 61.5 + - - +
93B SER 3.4 1.6 - - - -
94B SER* 4.0 4.3 - - - -
95B GLY 3.5 4.9 + - - -
130B ILE* 3.1 28.1 - - - +
152B GLY 4.6 0.2 - - - -
155B ILE* 3.5 11.1 - - - +
156B ASN* 3.3 25.1 - - - -
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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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76B MET* 3.6 25.1 - - - -
80B PHE* 5.3 1.3 - - + -
87B PRO* 3.0 10.6 + - + +
90B LEU* 4.2 18.4 - - + -
91B GLY* 1.3 77.4 - - - +
93B SER* 1.3 68.6 + - - +
95B GLY* 3.2 2.1 + - - -
96B ALA* 3.0 22.0 + - - +
126B GLY 4.7 0.2 - - - +
127B SER* 3.2 44.2 - - - +
130B ILE* 3.8 17.3 - - + +
131B SER* 3.1 30.3 - - - +
134B ILE* 4.9 1.6 - - + -
247B ILE* 3.8 14.6 - - + -
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Residues in contact with SER 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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69B LEU* 5.2 1.7 - - - +
87B PRO* 3.0 10.8 + - - +
88B GLY* 3.5 29.3 + - - -
92B ILE* 1.3 77.7 - - - +
94B SER* 1.3 57.1 + - - +
96B ALA* 3.1 4.0 + - - +
97B ALA* 2.9 29.1 + - - +
247B ILE* 3.8 6.7 - - - +
251B VAL* 3.5 28.9 - - - +
256B VAL* 4.1 19.1 - - - -
257B ILE 4.4 6.5 + - - -
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Residues in contact with SER 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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88B GLY* 5.9 0.7 - - - -
91B GLY* 4.0 6.3 + - - -
92B ILE 3.3 0.4 - - - -
93B SER* 1.3 76.8 - - - +
95B GLY* 1.3 57.5 + - - +
97B ALA* 3.7 6.6 - - - +
98B LEU* 2.9 30.3 + - - +
155B ILE* 4.5 2.7 - - - -
156B ASN* 2.9 31.8 + - - -
159B CYS* 3.9 28.7 - - - +
256B VAL* 4.3 14.6 - - - +
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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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91B GLY 3.5 5.9 + - - -
92B ILE 3.2 4.5 + - - -
93B SER 3.2 0.6 - - - -
94B SER* 1.3 76.5 - - - +
96B ALA* 1.3 64.3 + - - +
98B LEU* 3.4 6.3 + - - +
99B CYS* 3.0 28.1 + - - +
126B GLY* 4.1 8.1 - - - -
130B ILE* 3.5 26.4 - - - +
159B CYS* 4.6 2.4 - - - -
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Residues in contact with ALA 96 (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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92B ILE 3.0 13.4 + - - +
93B SER* 3.1 8.7 + - - +
95B GLY* 1.3 75.3 - - - +
97B ALA* 1.3 57.8 + - - +
99B CYS* 3.2 5.0 + - - +
100B VAL* 2.9 28.9 + - - +
123B ALA* 3.2 34.9 - - + +
126B GLY* 4.0 2.5 - - - -
127B SER* 4.0 9.0 - - - +
247B ILE* 4.9 1.6 - - + +
251B VAL* 3.6 22.4 - - + -
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Residues in contact with ALA 97 (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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93B SER 2.9 15.5 + - - +
94B SER* 3.7 5.2 - - - +
96B ALA* 1.3 74.9 - - - +
98B LEU* 1.3 58.1 + - - +
100B VAL* 2.9 12.4 + - - +
101B GLY 2.9 22.7 + - - -
178B PHE* 3.3 8.9 - - + -
181B TRP* 5.0 6.3 - - + -
182B SER* 4.8 15.0 - - - -
251B VAL* 3.7 10.9 - - + +
255B GLY 5.0 0.7 - - - +
256B VAL* 3.9 20.0 - - + -
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Residues in contact with LEU 98 (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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94B SER 2.9 18.7 + - - +
95B GLY* 3.7 4.9 - - - +
97B ALA* 1.3 75.6 - - - +
99B CYS* 1.3 58.4 + - - +
101B GLY* 3.4 3.9 + - - +
102B LEU* 2.9 45.1 + - + +
158B LEU* 5.2 8.1 - - + -
159B CYS* 3.7 33.4 - - + +
162B ALA* 4.5 18.4 - - + -
163B VAL* 4.9 12.1 - - + -
166B LEU* 6.4 2.0 - - + -
178B PHE* 5.1 4.3 - - + -
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Residues in contact with CYS 99 (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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95B GLY 3.0 11.5 + - - +
96B ALA 3.2 6.7 + - - +
98B LEU* 1.3 75.2 - - - +
100B VAL* 1.3 65.0 + - - +
102B LEU* 3.3 15.3 + - - +
103B ILE* 3.0 30.6 + - + +
122B GLY* 3.2 24.5 - - - +
125B ILE* 4.6 8.7 - - - -
126B GLY* 3.4 29.8 - - - -
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Residues in contact with VAL 100 (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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96B ALA 2.9 18.1 + - - +
97B ALA* 2.9 11.7 + - - +
99B CYS* 1.3 76.3 - - - +
101B GLY* 1.3 58.2 + - - +
103B ILE* 2.9 22.1 + - - +
104B ILE* 3.0 22.2 + - + +
119B HIS* 3.9 31.6 - - + +
123B ALA* 3.9 19.0 - - + +
178B PHE* 3.5 17.9 - - + -
181B TRP* 3.8 26.2 - - + -
251B VAL* 5.1 0.2 - - + -
252B ALA* 4.3 6.3 - - + +
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Residues in contact with GLY 101 (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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97B ALA 2.9 11.1 + - - -
98B LEU* 3.7 4.7 - - - -
99B CYS 3.3 0.2 - - - -
100B VAL* 1.3 75.3 - - - +
102B LEU* 1.3 58.0 + - - +
104B ILE* 3.1 7.4 + - - +
105B VAL* 3.0 38.5 + - - +
178B PHE* 3.4 27.5 - - - -
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Residues in contact with LEU 102 (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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98B LEU* 2.9 32.8 + - + +
99B CYS* 3.7 16.8 - - - +
100B VAL 3.2 0.2 - - - -
101B GLY* 1.3 76.1 - - - +
103B ILE* 1.3 66.4 + - + +
104B ILE 3.4 0.2 - - - -
105B VAL* 4.3 10.3 - - + +
106B MET* 4.0 26.6 + - + +
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Residues in contact with ILE 103 (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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99B CYS 3.0 15.7 + - - +
100B VAL* 2.9 12.8 + - - +
102B LEU* 1.3 86.7 - - + +
104B ILE* 1.3 60.6 + - + +
106B MET* 4.0 14.3 - - - -
118B SER* 3.6 45.8 - - - +
119B HIS* 4.9 5.6 + - + +
122B GLY* 4.3 11.7 - - - -
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Residues in contact with ILE 104 (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 VAL* 3.0 21.4 + - + +
101B GLY* 3.1 13.0 + - - +
103B ILE* 1.3 79.9 - - - +
105B VAL* 1.3 72.1 + - + +
106B MET 3.1 6.2 + - - -
119B HIS* 4.2 21.1 - - - +
174B GLN* 4.3 22.1 - - + +
175B LEU* 4.6 10.3 - - + -
178B PHE* 3.9 34.1 - - + -
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Residues in contact with VAL 105 (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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101B GLY* 3.0 23.6 + - - +
102B LEU* 4.9 10.3 - - + +
103B ILE 3.7 0.2 - - - -
104B ILE* 1.3 82.0 - - + +
106B MET* 1.3 65.5 + - + +
166B LEU* 5.1 12.8 - - + -
175B LEU* 4.9 14.4 - - + -
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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