Contacts of the helix formed by residues 602 - 608 (chain N) 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 SER 602 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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540N LEU* 4.1 5.4 - - - -
543N LEU* 4.1 2.7 - - - -
580N ALA 3.5 15.7 - - - -
581N LEU 3.4 16.8 - - - -
582N LEU 3.8 2.2 - - - -
583N ASP* 3.8 3.8 - - - -
584N ASN* 3.1 22.1 + - - -
600N LEU 3.5 1.4 + - - -
601N ARG* 1.3 73.1 - - - +
603N LEU* 1.3 65.4 + - - +
604N THR* 4.2 0.3 - - - -
605N ASP* 2.8 32.0 + - - -
606N ILE* 3.1 25.2 + - - +
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Residues in contact with LEU 603 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091M GLU* 4.2 19.2 - - + +
1094M ALA* 3.5 48.7 - - + +
1095M LEU* 3.8 23.6 - - + -
520N LEU* 4.6 2.2 - - + -
540N LEU* 3.7 28.2 - - + +
544N TYR* 4.6 5.2 - - - +
581N LEU* 3.4 22.3 + - + +
582N LEU* 3.9 10.3 - - + +
602N SER* 1.3 75.3 - - - +
604N THR* 1.3 64.1 + - - +
606N ILE* 3.2 12.9 + - + +
607N LEU* 3.0 26.2 + - - +
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Residues in contact with THR 604 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095M LEU* 4.1 0.5 - - - +
103N TRP* 2.8 41.1 + - + +
582N LEU 2.9 21.4 + - - -
583N ASP* 3.5 31.1 - - - +
602N SER 3.3 0.2 - - - -
603N LEU* 1.3 76.8 - - - +
605N ASP* 1.3 63.5 + - - +
607N LEU* 3.2 4.6 + - - +
608N SER* 2.8 38.6 + - - +
1444N THR* 4.3 13.7 - - + -
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Residues in contact with ASP 605 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583N ASP* 4.7 4.7 - - - +
584N ASN* 4.3 13.1 - - - +
599N PRO* 6.1 0.2 - - - +
600N LEU 3.8 9.2 - - - +
601N ARG* 3.4 30.5 + - + +
602N SER* 2.8 35.1 + - - +
604N THR* 1.3 78.1 - - - +
606N ILE* 1.3 62.5 + - - +
608N SER* 3.1 21.3 - - - +
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Residues in contact with ILE 606 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1091M GLU* 3.2 35.9 - - + +
524N LEU 6.0 1.1 - - - +
538N SER* 5.7 1.8 - - - +
540N LEU* 3.8 31.0 - - + -
601N ARG* 3.8 32.0 + - + +
602N SER 3.1 16.5 + - - +
603N LEU* 3.4 13.9 - - + +
605N ASP* 1.3 77.2 - - - +
607N LEU* 1.3 53.3 + - + +
612N GLY* 3.2 4.9 - - - -
613N ARG* 2.7 48.9 + - - +
318P GLU* 5.8 3.1 - - - +
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Residues in contact with LEU 607 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088M LEU* 3.5 28.3 - - + -
1091M GLU* 4.4 19.1 - - + +
1092M LEU* 3.4 33.0 - - + -
1095M LEU* 3.6 19.7 - - + -
103N TRP* 4.4 3.6 - - + -
603N LEU 3.0 14.9 + - - +
604N THR* 3.7 8.5 - - - +
606N ILE* 1.3 78.8 - - + +
608N SER* 1.3 60.6 + - - +
609N GLY 5.0 0.2 - - - +
612N GLY* 3.8 0.5 - - - -
613N ARG* 3.4 24.7 + - + +
614N PHE* 3.7 25.0 + - + +
1443N THR* 4.9 6.7 - - + -
1447N LEU* 4.3 11.9 - - + -
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Residues in contact with SER 608 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604N THR* 2.8 31.6 + - - +
605N ASP* 3.1 17.5 - - - +
607N LEU* 1.3 78.8 - - - +
609N GLY* 1.3 62.8 + - - +
611N GLN* 5.8 0.2 - - - +
612N GLY* 3.6 7.0 + - - -
614N PHE* 5.7 0.2 - - - -
1443N THR* 3.5 31.6 - - - -
1444N THR* 5.1 3.8 - - - +
12Q G 5.9 2.9 - - - -
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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