Contacts of the helix formed by residues 102 - 107 (chain D) in PDB entry 4G7H
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 ILE 102 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100D ALA 3.4 4.6 + - - -
101D HIS* 1.3 73.4 + - - +
103D TRP* 1.3 63.1 + - + +
105D VAL* 3.5 8.5 - - + -
106D LYS* 2.7 49.7 + - + +
128D TYR* 4.4 3.4 - - - +
579D ASP* 3.2 40.1 + - + +
582D LEU* 4.4 9.5 - - + +
583D ASP* 3.8 33.7 - - + +
586D ARG* 3.7 19.5 - - + -
587D ARG* 3.7 27.8 - - + +
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Residues in contact with TRP 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095C LEU* 3.7 32.6 - - + +
1097C LEU* 3.6 31.0 - - + -
101D HIS* 3.0 25.2 + + + +
102D ILE* 1.3 85.2 - - + +
104D PHE* 1.3 64.6 + + + +
105D VAL 3.4 1.0 + - - -
107D ASP* 3.1 31.6 - - - +
111D LYS* 5.6 0.5 - - - +
582D LEU* 4.8 0.4 + - + -
583D ASP* 3.8 12.7 + - + +
586D ARG* 6.0 0.9 - - + -
604D THR* 2.9 32.3 + - + -
607D LEU* 4.5 4.0 - - + -
1443D THR* 5.7 1.3 - - + -
1444D THR* 3.5 30.2 - - + +
1447D LEU* 3.9 29.2 - - + -
1448D THR* 3.5 31.3 - - + +
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Residues in contact with PHE 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097C LEU* 4.4 14.1 - - + -
12D LEU* 3.6 32.8 - - + -
101D HIS* 3.0 46.3 + + + +
103D TRP* 1.3 76.5 - + + +
105D VAL* 1.3 59.3 + - - +
107D ASP 5.0 0.4 - - - -
110D SER* 3.2 15.2 + - - -
111D LYS* 3.6 16.1 + - + -
112D ILE* 3.5 18.8 + - + +
512D MET* 3.6 42.2 - - + -
1448D THR* 3.9 39.5 - - + -
1451D ALA* 4.9 1.3 - - + -
1452D ILE* 4.1 10.8 - - + -
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Residues in contact with VAL 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ALA* 3.7 20.4 - - + -
101D HIS 3.7 7.2 - - - +
102D ILE* 2.9 11.6 + - + +
104D PHE* 1.3 82.8 - - - +
106D LYS* 1.3 77.3 + - + +
107D ASP 3.3 1.7 - - - -
108D VAL* 5.6 1.2 - - - +
110D SER* 3.2 25.7 - - - -
112D ILE* 3.9 9.9 - - + -
123D LEU* 4.4 12.1 - - + +
124D GLU* 5.9 2.7 - - - +
127D LEU* 3.6 34.1 - - + -
128D TYR* 5.3 9.2 - - + +
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Residues in contact with LYS 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ILE* 2.7 33.0 + - + +
105D VAL* 1.3 85.2 - - + +
107D ASP* 1.3 59.2 + - - +
108D VAL* 3.5 14.0 + - - +
124D GLU* 4.1 15.5 - - - -
128D TYR* 5.8 0.9 - - + +
586D ARG* 3.0 47.0 + - + +
587D ARG* 3.8 31.2 - - + +
10G G 4.1 17.1 + - - +
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Residues in contact with ASP 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D ILE 4.1 0.2 + - - -
103D TRP* 3.1 23.7 + - + +
105D VAL 3.3 1.2 - - - -
106D LYS* 1.3 77.4 - - - +
108D VAL* 1.3 63.1 + - - +
109D PRO 3.2 16.3 - - - +
110D SER* 3.3 7.7 + - - -
111D LYS* 4.4 11.6 + - - +
586D ARG* 4.5 4.5 - - - +
1444D THR* 4.5 8.0 + - - +
1445D HIS* 3.4 45.5 + - - +
1448D THR* 3.5 18.3 + - + +
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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