Contacts of the helix formed by residues 1078 - 1087 (chain B) in PDB entry 2QRA
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 SER1078 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1073B TRP* 4.6 1.1 - - - -
1076B GLY 3.4 2.6 + - - -
1077B ASP* 1.3 74.6 - - - +
1079B ALA* 1.3 55.2 + - - +
1080B VAL* 3.6 4.2 + - - +
1081B GLY* 2.7 32.4 + - - -
1082B ARG* 2.7 39.0 + - - +
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Residues in contact with ALA1079 (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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1042B VAL* 5.9 1.7 - - + +
1046B THR* 3.6 31.6 - - + +
1047B LEU* 3.8 19.5 - - + -
1050B ALA* 3.7 19.5 - - + -
1052B PHE* 3.6 7.6 - - - -
1073B TRP* 3.9 12.1 - - + -
1077B ASP 3.9 3.6 + - - -
1078B SER* 1.3 72.1 + - - +
1080B VAL* 1.3 64.6 + - + +
1082B ARG* 3.6 1.4 + - - +
1083B HIS* 3.1 22.0 + - - +
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Residues in contact with VAL1080 (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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1049B ARG* 5.6 1.1 - - + -
1050B ALA* 3.9 23.3 - - + +
1078B SER* 3.3 3.9 + - - +
1079B ALA* 1.3 74.3 - - + +
1081B GLY* 1.3 58.8 + - - +
1083B HIS* 3.0 8.1 + - - +
1084B ARG* 2.7 55.6 + - - +
1092B PHE* 5.8 0.9 - - + -
1093B ILE* 3.9 19.3 - - + -
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Residues in contact with GLY1081 (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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1078B SER* 2.7 26.5 + - - -
1080B VAL* 1.3 80.3 - - - +
1082B ARG* 1.3 61.8 + - - +
1084B ARG* 3.5 7.3 + - - +
1085B LYS* 3.3 20.1 + - - +
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Residues in contact with ARG1082 (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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1070B VAL* 3.2 28.1 - - + +
1071B ASP* 2.8 31.1 + - - +
1072B ARG 3.8 0.4 + - - -
1073B TRP* 3.5 30.9 - - + -
1077B ASP* 3.6 26.2 - - - +
1078B SER 2.7 23.1 + - - +
1079B ALA 4.3 0.4 - - - +
1081B GLY* 1.3 72.6 - - - -
1083B HIS* 1.3 58.4 + - - +
1085B LYS* 2.9 30.5 + - + +
1086B VAL* 3.1 14.0 + - + +
3071D ASP* 3.5 26.7 + - - -
3072D ARG* 3.4 37.7 - - - +
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Residues in contact with HIS1083 (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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1050B ALA 2.8 28.7 + - - -
1052B PHE* 3.6 21.5 - + + -
1063B CYS* 3.1 16.8 - - + +
1066B CYS* 4.2 5.6 - - - -
1068B ALA* 5.2 0.4 - - + -
1079B ALA 3.1 16.4 + - - +
1080B VAL* 3.0 12.0 + - - +
1082B ARG* 1.3 72.4 - - - +
1084B ARG* 1.3 64.0 + - - +
1085B LYS 2.9 5.5 + - - -
1086B VAL* 3.2 11.7 + - + +
1087B SER* 3.1 19.0 + - - +
1090B CYS* 3.7 3.1 - - + -
1092B PHE* 4.0 2.7 - + - -
1093B ILE* 3.1 26.4 - - + +
1100B ZN 2.2 36.6 - - - -
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Residues in contact with ARG1084 (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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1080B VAL* 2.7 36.0 + - - +
1081B GLY* 3.9 7.0 - - - +
1083B HIS* 1.3 72.9 - - - +
1085B LYS* 1.3 57.8 + - - +
1087B SER 4.1 6.7 - - - -
1088B PRO* 2.9 49.2 + - + +
1093B ILE* 3.0 42.7 + - + +
1094B ASN* 4.7 7.9 + - - -
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Residues in contact with LYS1085 (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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1081B GLY 3.3 10.6 + - - +
1082B ARG* 2.9 25.3 - - + +
1083B HIS 2.9 1.0 - - - -
1084B ARG* 1.3 81.6 - - - +
1086B VAL* 1.3 64.0 + - + +
1087B SER 3.1 1.1 + - - -
1088B PRO* 4.0 3.5 - - - +
3057D GLU* 3.8 29.4 + - - +
3060D THR* 3.4 32.4 + - - -
3062D ARG* 3.8 13.3 + - - -
3069D ALA* 5.4 0.2 - - - +
3071D ASP* 3.9 14.4 + - - -
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Residues in contact with VAL1086 (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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1068B ALA* 3.7 25.1 - - + +
1069B ALA 4.9 3.4 - - - +
1070B VAL* 4.0 24.9 - - + -
1082B ARG* 3.9 10.8 - - + +
1083B HIS* 3.5 13.5 - - + +
1085B LYS* 1.3 81.8 - - + +
1087B SER* 1.3 69.7 + - - +
1088B PRO* 4.2 0.2 - - - -
3060D THR* 6.1 0.7 - - + -
3062D ARG* 3.3 21.1 + - - -
3067D HIS 4.8 0.7 - - - +
3069D ALA* 4.2 35.9 + - + +
3070D VAL* 6.0 0.2 - - - -
3071D ASP* 5.5 7.4 - - - +
5001D EOH 5.1 2.6 + - - -
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Residues in contact with SER1087 (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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1066B CYS* 4.1 19.6 - - - -
1068B ALA* 3.2 22.3 - - - +
1083B HIS 3.1 13.1 + - - +
1084B ARG* 3.4 6.3 - - - -
1085B LYS 3.1 0.8 - - - -
1086B VAL* 1.3 89.3 + - - +
1088B PRO* 1.3 69.7 - - - +
1089B ASN 3.0 11.2 + - - +
1090B CYS* 3.5 18.7 - - - +
1093B ILE* 5.0 0.7 - - - +
3062D ARG* 5.2 0.7 - - - +
5001D EOH 4.2 7.9 + - - -
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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