Contacts of the helix formed by residues 612 - 618 (chain D) in PDB entry 5D4D
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 612 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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601D ARG* 4.4 0.2 - - - -
605D ASP 4.3 0.9 - - - -
606D ILE 3.3 9.4 - - - -
607D LEU 3.2 15.9 - - - -
608D SER 3.4 8.8 + - - -
609D GLY 2.8 14.4 + - - -
610D LYS 3.2 0.2 - - - -
611D GLN* 1.3 79.4 - - - +
613D ARG* 1.3 62.3 + - - -
614D PHE 3.4 1.1 - - - -
616D GLN* 2.9 28.7 + - - +
617D ASN* 4.7 0.9 - - - -
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Residues in contact with ARG 613 (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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1016C ILE* 3.9 21.4 - - - +
1017C THR* 3.3 21.5 - - - +
1084C SER* 4.6 6.1 - - - +
1087C VAL* 3.6 12.7 - - - +
1088C LEU* 4.5 13.9 - - + -
1091C GLU* 2.8 42.1 + - - +
601D ARG* 5.6 3.6 - - - +
606D ILE* 2.7 31.3 + - - +
607D LEU* 3.0 17.0 + - + -
612D GLY* 1.3 70.5 - - - -
614D PHE* 1.3 65.8 + - + +
617D ASN* 2.9 48.5 + - - -
618D LEU* 3.3 25.4 + - + +
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Residues in contact with PHE 614 (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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1088C LEU* 3.7 39.9 - - + -
1092C LEU* 5.1 5.8 - - + -
607D LEU* 3.9 23.5 + - + +
608D SER* 5.6 0.2 - - - -
612D GLY 3.4 0.6 - - - -
613D ARG* 1.3 76.9 - - - +
615D ARG* 1.3 62.0 + - + +
618D LEU* 2.9 21.5 + - + -
619D LEU* 2.8 30.2 + - + -
1434D TRP* 5.4 2.2 - + - -
1435D LEU* 4.3 12.3 - - + -
1438D ALA* 4.3 21.5 - - + -
1439D SER* 3.7 32.5 - - - -
1443D THR* 4.0 22.4 - - + -
1447D LEU* 5.0 3.6 - - + -
1467D ILE* 3.8 19.7 - - + -
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Residues in contact with ARG 615 (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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1031C ARG* 3.2 13.9 + - - -
1034C GLU* 3.0 28.3 + - - +
609D GLY* 3.8 23.6 + - - +
610D LYS* 3.9 34.0 - - + +
612D GLY 3.9 2.0 + - - -
613D ARG 3.6 0.2 - - - -
614D PHE* 1.3 82.4 - - + +
616D GLN* 1.3 61.7 + - - +
619D LEU* 4.4 5.8 - - + -
620D GLY 4.1 8.1 + - - -
1096D ARG* 3.5 50.0 - - - +
1439D SER 4.0 12.3 - - - +
1440D PHE 4.6 3.0 + - - -
13G G 3.2 27.1 + - - -
14G A 4.7 5.9 + - - -
15G G 3.6 22.4 + - - -
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Residues in contact with GLN 616 (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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1031C ARG* 2.6 51.7 + - - +
610D LYS* 3.7 16.9 - - - +
611D GLN* 3.9 28.0 + - + +
612D GLY 2.9 21.0 + - - +
615D ARG* 1.3 79.3 - - - +
617D ASN* 1.3 69.8 + - - +
620D GLY 2.7 11.9 - - - +
621D LYS* 4.3 0.3 - - - -
622D ARG* 5.8 4.2 - - - +
331F ASP* 5.6 4.0 + - - -
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Residues in contact with ASN 617 (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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1017C THR* 3.4 21.5 + - - +
1019C GLN* 2.8 45.9 + - - +
1031C ARG* 5.4 0.4 - - - +
1084C SER* 3.8 10.5 - - - +
611D GLN 5.4 0.3 - - - +
612D GLY 4.1 0.5 - - - +
613D ARG* 2.9 46.3 + - - +
616D GLN* 1.3 90.5 + - - +
618D LEU* 1.3 66.1 + - - +
620D GLY 3.3 8.7 - - - -
621D LYS* 3.4 6.4 - - - -
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Residues in contact with LEU 618 (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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1053C LEU* 4.5 0.7 - - - +
1082C PRO* 6.0 0.4 - - + -
1084C SER* 3.7 28.0 - - - +
1085C PHE* 4.0 4.9 - - + +
1088C LEU* 4.2 22.7 - - + -
613D ARG* 3.3 39.9 + - + +
614D PHE* 2.9 17.0 + - + +
617D ASN* 1.3 86.1 - - - +
619D LEU* 1.3 64.3 + - - +
620D GLY 3.1 6.2 + - - -
621D LYS* 3.9 16.7 + - - +
1466D VAL* 3.8 21.1 - - - +
1467D ILE* 4.0 36.6 - - + +
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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