Contacts of the helix formed by residues 1072 - 1082 (chain B) in PDB entry 5YS0
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 PRO1072 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1070B PRO 4.9 0.2 - - - +
1071B VAL* 1.3 94.6 - - + +
1073B LEU* 1.3 67.9 + - - +
1074B GLY 3.1 2.9 - - - +
1075B THR* 2.8 28.6 + - - +
1076B VAL 3.4 7.0 + - - -
1176B ASN* 3.1 44.6 - - + +
1178B THR* 4.3 1.1 - - - -
1156C VAL 5.2 4.0 - - - +
1157C PRO* 4.5 15.9 - - + +
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Residues in contact with LEU1073 (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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1072B PRO* 1.3 71.0 - - - +
1074B GLY* 1.3 59.3 + - - +
1076B VAL* 3.3 5.2 + - - +
1077B PHE* 2.9 24.9 + - - +
1141B LEU* 3.6 34.8 - - + +
1143B SER* 3.3 27.8 - - - +
1144B PHE* 4.2 2.0 - - - +
1145B PHE* 3.5 23.2 - - + -
1170B TYR 3.4 31.9 - - - +
1171B SER 3.9 4.5 - - - +
1172B TRP* 4.3 15.7 - - + +
1176B ASN* 5.1 1.5 + - - +
1177B THR 3.8 3.2 + - - +
1178B THR* 3.6 24.0 - - - +
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Residues in contact with GLY1074 (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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1072B PRO* 2.8 7.9 + - - +
1073B LEU* 1.3 77.2 - - - +
1075B THR* 1.3 57.9 + - - -
1077B PHE* 3.7 12.0 - - - +
1078B SER* 3.5 18.7 + - - -
1141B LEU* 4.1 14.6 - - - -
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Residues in contact with THR1075 (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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1071B VAL* 3.6 24.6 - - + +
1072B PRO* 2.8 20.0 + - - +
1074B GLY* 1.3 70.7 - - - -
1076B VAL* 1.3 57.1 + - - -
1077B PHE 3.0 1.3 - - - -
1078B SER* 2.8 4.9 + - - +
1079B LEU* 2.7 49.0 + - + +
1221B ILE* 5.0 1.1 - - + -
1157C PRO* 3.7 28.5 - - + +
1158C TYR* 6.1 0.4 - - + -
1194C LEU* 3.9 28.7 - - + -
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Residues in contact with VAL1076 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1069B ILE* 3.4 18.8 - - + -
1071B VAL* 3.6 13.9 - - + +
1072B PRO 3.4 2.4 + - - +
1073B LEU 3.3 9.8 + - - +
1075B THR* 1.3 76.3 - - - +
1077B PHE* 1.3 61.2 + - - +
1079B LEU* 4.5 7.0 - - + -
1080B LEU* 3.3 32.3 + - + +
1081B TYR* 4.4 0.5 - - - -
1145B PHE* 4.6 1.6 - - + -
1170B TYR* 3.7 38.1 - - + -
1178B THR* 3.4 33.7 - - + +
1217B LEU* 4.4 6.7 - - + -
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Residues in contact with PHE1077 (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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1073B LEU 2.9 15.5 + - - +
1074B GLY* 3.8 12.1 - - - +
1075B THR 3.0 0.6 - - - -
1076B VAL* 1.3 80.0 - - - +
1078B SER* 1.3 65.7 + - - +
1081B TYR* 2.8 50.3 + + + -
1082B GLY* 3.1 3.7 + - - -
1136B ILE* 3.7 27.4 - - + -
1139B MET* 3.7 33.2 - - + -
1141B LEU* 4.6 10.3 - - + -
1145B PHE* 3.2 46.4 - + + -
1147B VAL* 5.2 0.2 - - + -
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Residues in contact with SER1078 (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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1074B GLY 3.5 14.2 + - - -
1075B THR* 2.8 6.5 + - - -
1077B PHE* 1.3 81.0 - - - +
1079B LEU* 1.3 68.8 + - - +
1082B GLY* 3.0 29.3 + - - +
1084B ASP* 4.6 5.0 - - - +
1087B TYR* 5.1 2.3 - - - -
1194C LEU* 4.7 13.7 - - - -
1197C THR* 5.3 10.2 - - - +
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Residues in contact with LEU1079 (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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1071B VAL* 4.9 0.7 - - + -
1075B THR* 2.7 34.1 + - + +
1076B VAL* 4.0 6.1 - - - +
1078B SER* 1.3 76.2 - - - +
1080B LEU* 1.3 60.1 + - + +
1082B GLY 4.6 0.2 + - - -
1084B ASP 4.6 2.4 - - - +
1085B THR* 5.8 0.3 - - - -
1087B TYR* 3.2 53.3 - - + +
1088B ILE* 3.9 3.6 + - - +
1217B LEU* 4.1 24.0 - - + -
1220B ILE* 4.1 15.0 - - + -
1221B ILE* 3.5 31.0 - - + -
1193C MET* 5.3 1.1 - - + -
1194C LEU* 3.6 27.1 - - + -
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Residues in contact with LEU1080 (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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1076B VAL* 3.3 16.1 + - + +
1079B LEU* 1.3 78.5 - - + +
1081B TYR* 1.3 78.8 + - + +
1082B GLY 3.6 0.8 - - - +
1087B TYR* 6.0 0.7 - - + -
1088B ILE* 3.5 29.6 - - + +
1091B ILE* 4.6 8.5 - - + -
1111B ARG* 2.9 20.3 + - - -
1170B TYR* 3.4 34.5 - - + +
1213B LEU* 4.1 19.5 - - + -
1217B LEU* 3.6 47.1 - - + -
1220B ILE* 6.3 0.4 - - + -
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Residues in contact with TYR1081 (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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1077B PHE* 2.8 37.5 + + + +
1080B LEU* 1.3 98.0 - - + +
1082B GLY* 1.3 67.5 + - - +
1083B ASP* 3.9 1.6 + - - +
1088B ILE* 5.5 3.1 - - + -
1106B PHE* 3.6 31.0 - + + -
1111B ARG* 3.8 14.8 - - - +
1134B GLU* 3.4 26.4 + - - -
1136B ILE* 5.0 0.4 - - + -
1145B PHE* 3.7 18.6 - + - -
1147B VAL* 3.4 29.1 - - + +
1168B PHE* 4.1 6.9 - - - +
1170B TYR* 2.3 49.4 + + - -
1213B LEU* 5.7 0.3 - - - +
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Residues in contact with GLY1082 (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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1077B PHE* 3.1 6.4 + - - -
1078B SER* 3.0 36.0 + - - -
1079B LEU 4.5 0.4 + - - -
1080B LEU 3.6 1.3 - - - +
1081B TYR* 1.3 83.5 - - - +
1083B ASP* 1.3 59.4 + - - -
1084B ASP 3.1 13.7 + - - +
1085B THR* 3.7 15.9 - - - +
1105B LYS* 5.6 0.5 - - - +
1111B ARG* 4.3 2.9 + - - -
1197C THR* 6.3 0.4 - - - -
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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