Contacts of the helix formed by residues 1075 - 1085 (chain B) in PDB entry 1XTB
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 GLY1075 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1072B LYS 2.9 15.1 + - - -
1073B SER 3.2 3.0 + - - -
1074B ARG* 1.3 78.9 - - - +
1076B VAL* 1.3 64.1 + - - +
1077B GLU 3.3 2.7 - - - -
1078B ALA* 3.4 12.4 + - - +
1079B ALA* 3.0 24.9 + - - +
1502B VAL* 4.1 0.8 - - - +
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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
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1071B ALA* 3.2 35.5 + - + +
1072B LYS* 4.4 1.0 + - - +
1074B ARG* 3.4 1.1 - - + -
1075B GLY* 1.3 74.7 - - - +
1077B GLU* 1.3 61.6 + - + +
1079B ALA* 3.3 2.8 + - - +
1080B ARG* 2.9 28.8 + - + +
1306B PHE* 5.0 7.0 - - + -
1311B LEU* 4.5 15.7 - - + -
1317B VAL* 4.8 4.9 - - + -
1498B PHE* 4.5 2.8 - - + -
1499B VAL* 4.0 40.6 - - + -
1502B VAL* 4.0 20.6 - - + -
1503B VAL* 4.3 7.6 - - + -
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Residues in contact with GLU1077 (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 LYS* 3.7 28.5 + - - +
1075B GLY 3.3 0.6 - - - -
1076B VAL* 1.3 76.5 - - - +
1078B ALA* 1.3 62.7 + - - +
1080B ARG* 3.2 31.6 + - - +
1081B GLU* 3.1 28.4 + - - +
1309B THR 5.7 0.9 - - - +
1310B PRO* 5.8 1.6 - - - +
1311B LEU* 3.7 43.2 + - + +
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Residues in contact with ALA1078 (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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1075B GLY* 3.4 13.5 + - - +
1076B VAL 3.4 0.2 - - - -
1077B GLU* 1.3 78.6 - - - +
1079B ALA* 1.3 60.5 + - - +
1081B GLU* 3.5 8.3 + - - +
1082B SER* 3.0 28.2 + - - -
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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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1075B GLY 3.0 17.5 + - - +
1076B VAL 3.6 4.3 - - - +
1077B GLU 3.2 0.2 - - - -
1078B ALA* 1.3 73.6 - - - +
1080B ARG* 1.3 66.8 + - - +
1082B SER* 3.2 8.9 + - - -
1083B MET* 3.0 17.7 + - - +
1089B ILE* 4.7 3.1 - - + +
1365B LYS* 6.4 0.2 - - - +
1498B PHE* 3.5 11.2 - - + -
1502B VAL* 3.8 30.7 - - + -
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Residues in contact with ARG1080 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1076B VAL* 2.9 15.3 + - - +
1077B GLU* 3.4 43.7 + - - +
1079B ALA* 1.3 77.1 - - - +
1081B GLU* 1.3 86.0 + - - +
1083B MET* 3.1 3.5 + - - +
1084B PHE* 3.0 39.6 + - + -
1306B PHE* 2.9 59.3 + - + -
1307B ARG* 3.4 26.6 + - - +
1309B THR 4.4 5.7 + - - -
1311B LEU* 4.9 4.0 - - - +
1314B ASN* 4.2 7.3 - - - +
1498B PHE* 3.6 16.3 - - + -
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Residues in contact with GLU1081 (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 GLU* 3.1 14.9 + - + +
1078B ALA* 3.8 8.5 - - - +
1079B ALA 3.3 0.2 - - - -
1080B ARG* 1.3 111.2 + - - +
1082B SER* 1.3 57.2 + - - +
1084B PHE* 3.3 2.5 + - - +
1085B ASN* 2.8 46.4 + - - +
1307B ARG* 3.0 43.2 + - - +
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Residues in contact with SER1082 (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 ALA 3.0 16.5 + - - -
1079B ALA* 3.5 11.5 - - - -
1080B ARG 3.2 0.2 - - - -
1081B GLU* 1.3 76.9 - - - +
1083B MET* 1.3 62.8 + - - +
1085B ASN 3.5 0.2 + - - -
1086B GLY 3.5 1.4 + - - -
1087B GLU* 2.9 61.2 + - - +
1089B ILE* 3.7 17.7 - - - -
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Residues in contact with MET1083 (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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1079B ALA 3.0 12.3 + - - +
1080B ARG 3.1 4.9 + - - +
1082B SER* 1.3 76.1 - - - +
1084B PHE* 1.3 89.8 + - + +
1086B GLY* 3.1 12.3 + - - -
1087B GLU 4.5 1.1 + - - +
1089B ILE* 3.5 22.4 - - + +
1097B VAL* 3.3 36.8 - - - +
1098B LEU* 3.3 14.6 - - - +
1099B HIS* 4.2 12.3 - - - -
1100B VAL* 4.4 7.0 - - + -
1495B HIS* 4.0 23.1 - - + +
1498B PHE* 4.0 35.9 - - + -
1509B PHE* 4.5 0.9 - - - -
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Residues in contact with PHE1084 (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 ARG* 3.0 46.2 + - + +
1081B GLU 3.9 0.7 - - - +
1083B MET* 1.3 101.5 - - + +
1085B ASN* 1.3 59.2 + - - +
1086B GLY 3.2 3.7 + - - -
1098B LEU* 4.1 1.4 - - - +
1100B VAL* 3.9 32.5 - - + -
1110B ILE* 3.6 24.6 - - + +
1303B ASP* 3.9 40.6 - - + -
1306B PHE* 4.0 10.3 - + - -
1307B ARG* 3.5 47.3 + - + +
1495B HIS* 4.3 1.6 - + - -
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Residues in contact with ASN1085 (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 GLU* 2.8 42.6 + - - +
1082B SER 4.2 2.9 - - - +
1083B MET 3.2 0.4 - - - -
1084B PHE* 1.3 72.1 - - - +
1086B GLY* 1.3 61.5 + - - +
1087B GLU* 3.3 19.8 + - + +
1110B ILE* 4.3 6.7 - - - +
1111B VAL 3.8 13.4 + - - +
1307B ARG* 3.4 19.2 + - - +
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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