Contacts of the helix formed by residues 102 - 110 (chain B) in PDB entry 4GCK
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 ASN 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B PHE* 4.8 5.2 - - - -
98B PHE* 2.9 50.8 + - + +
99B GLY 3.2 3.8 + - - -
101B ARG* 1.3 97.6 - - - +
103B PRO* 1.3 65.9 - - - +
104B GLY 3.3 2.7 - - - -
105B LEU* 3.0 34.9 + - + +
106B THR* 2.9 20.4 + - - -
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Residues in contact with PRO 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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24B GLU* 4.0 28.9 - - + +
99B GLY 3.4 6.2 - - - +
100B GLU 3.4 15.9 - - - +
101B ARG 3.5 4.7 - - - +
102B ASN* 1.3 86.3 - - - +
104B GLY* 1.3 64.0 + - - +
106B THR* 3.1 14.0 + - - +
107B ARG* 3.1 9.7 + - - +
173B PHE* 4.0 11.9 - - + -
178B PHE* 3.6 44.1 - - + -
181B ARG* 5.0 4.3 - - - +
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Residues in contact with GLY 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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20B ALA* 4.0 5.4 - - - -
23B LEU* 3.4 25.9 - - - +
24B GLU* 3.4 31.5 - - - +
102B ASN 3.3 1.2 - - - -
103B PRO* 1.3 79.6 - - - +
105B LEU* 1.3 62.6 + - - +
107B ARG* 3.3 17.8 - - - +
108B ILE* 3.7 2.8 + - - +
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Residues in contact with LEU 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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20B ALA* 4.6 15.7 - - + -
23B LEU* 5.7 0.4 - - + -
62B LEU* 3.7 40.6 - - + +
65B PHE* 3.7 35.7 - - + -
66B ILE* 3.7 16.7 - - + +
98B PHE* 4.0 11.0 - - + -
102B ASN* 3.0 32.0 + - + +
104B GLY* 1.3 73.1 - - - +
106B THR* 1.3 61.1 + - - +
107B ARG 3.1 2.2 - - - -
108B ILE* 2.8 28.8 + - + +
109B LEU* 3.0 10.8 + - - +
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Residues in contact with THR 106 (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 GLY* 2.7 38.5 + - - -
102B ASN 2.9 6.6 + - - -
103B PRO* 3.1 12.3 + - - -
105B LEU* 1.3 75.3 - - - +
107B ARG* 1.3 56.4 - - - +
109B LEU* 3.0 11.5 + - + +
110B THR* 2.9 36.4 + - + -
170B LEU* 4.1 19.5 - - + -
173B PHE* 3.9 15.5 - - + -
174B VAL* 3.7 20.0 - - + -
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Residues in contact with ARG 107 (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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115A MET* 5.4 3.3 - - - +
23B LEU* 2.8 19.1 + - + +
25B SER 3.5 18.8 + - - -
26B SER* 4.9 3.4 - - - +
28B GLY* 3.1 27.1 + - - -
29B SER* 3.8 19.9 - - - +
103B PRO 3.1 5.0 + - - +
104B GLY 3.3 13.0 - - - +
106B THR* 1.3 78.2 - - - +
108B ILE* 1.3 57.2 + - - +
110B THR* 3.4 7.2 + - - -
112B HIS* 3.2 16.5 + - + +
113B ALA* 2.9 38.4 + - + +
174B VAL* 4.1 30.8 + - + +
177B GLU* 5.2 10.7 - - - +
178B PHE* 3.3 40.6 - - + -
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Residues in contact with ILE 108 (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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23B LEU* 4.2 6.3 - - + -
59B PHE* 3.7 35.7 - - + +
62B LEU* 3.8 33.4 - - + -
63B ILE* 3.9 25.1 - - + -
66B ILE* 4.2 6.3 - - + -
104B GLY 4.1 5.4 - - - +
105B LEU* 2.8 20.4 + - + +
107B ARG* 1.3 77.2 - - - +
109B LEU* 1.3 60.1 + - - +
111B GLY* 3.0 19.8 + - - -
113B ALA* 4.2 8.1 - - + -
114B LEU* 3.8 21.6 - - + +
125B ILE* 3.9 12.6 - - + +
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Residues in contact with LEU 109 (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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175A ARG* 5.4 0.9 - - - -
66B ILE* 4.3 20.2 - - + -
70B LEU* 5.5 3.1 - - + -
95B ILE* 5.5 6.7 - - + +
98B PHE* 5.1 12.6 - - + -
99B GLY* 5.4 2.9 - - - -
105B LEU 3.0 9.6 + - - +
106B THR* 3.0 19.9 + - + +
108B ILE* 1.3 78.6 - - - +
110B THR* 1.3 62.7 + - + +
111B GLY 3.4 0.5 + - - -
122B GLN* 5.2 0.9 + - - -
125B ILE* 3.5 16.9 - - + +
128B LEU* 4.3 23.1 - - + -
129B PHE* 3.3 56.6 - - + -
132B ILE* 6.3 0.9 - - + -
170B LEU* 4.1 21.3 - - + -
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Residues in contact with THR 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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112A HIS* 2.7 32.1 + - - -
171A SER* 4.9 8.6 + - - +
175A ARG* 6.0 3.2 - - - +
106B THR* 2.9 19.0 + - + +
107B ARG 3.4 5.9 + - - -
109B LEU* 1.3 76.0 - - + +
111B GLY* 1.3 51.8 + - - +
112B HIS* 2.7 29.4 + - - -
122B GLN* 4.9 1.3 - - - +
129B PHE* 5.7 0.7 - - + -
167B GLU* 5.3 1.1 - - - +
170B LEU* 3.9 31.9 - - + -
171B SER* 4.1 6.3 - - - +
174B VAL* 3.6 22.1 - - + +
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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
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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