Contacts of the strand formed by residues 1098 - 1104 (chain B) in PDB entry 5M5X
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 TYR1098 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 3.5 39.5 - - + +
2A ASP 4.4 3.8 + - - -
5A LYS* 3.7 7.4 + - + -
7A VAL* 5.4 2.7 - - + +
1093B LEU 2.8 17.5 + - - +
1094B ASN* 3.2 38.1 - - - +
1095B SER 5.4 0.7 - - - -
1096B SER 3.3 6.1 - - - +
1097B ASP* 1.3 72.7 - - - +
1099B THR* 1.3 60.8 + - - +
1100B GLN* 2.4 42.6 + - + +
1177B ALA* 3.6 28.0 - - + +
1178B ILE 4.4 4.0 - - - -
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Residues in contact with THR1099 (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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1097B ASP 3.0 9.0 + - - +
1098B TYR* 1.3 77.4 - - - +
1100B GLN* 1.3 68.5 + - - +
1101B ALA* 3.3 9.8 + - + +
1177B ALA* 4.6 0.7 - - - -
1178B ILE* 2.8 43.5 + - + +
1180B PHE* 3.7 34.2 - - + +
1183B LYS* 5.4 2.6 + - - +
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Residues in contact with GLN1100 (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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5A LYS* 3.2 60.3 + - - +
6A PRO 5.0 6.0 + - - +
7A VAL* 5.2 3.5 - - - +
1098B TYR* 2.4 41.8 + - + +
1099B THR* 1.3 74.2 + - - +
1101B ALA* 1.3 65.4 + - - +
1175B THR* 5.0 16.7 + - - +
1176B VAL 3.5 9.6 - - - +
1177B ALA* 4.5 8.5 - - + +
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Residues in contact with ALA1101 (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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1099B THR* 3.3 7.7 + - + +
1100B GLN* 1.3 76.5 - - - +
1102B SER* 1.3 61.7 + - - +
1103B VAL* 5.0 1.3 - - + -
1110B ILE* 3.9 13.2 - - + -
1175B THR* 3.3 6.4 - - - -
1176B VAL 3.0 29.8 + - - -
1178B ILE* 3.7 21.3 - - + -
1183B LYS* 3.7 26.9 - - - +
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Residues in contact with SER1102 (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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1101B ALA* 1.3 75.7 - - - +
1103B VAL* 1.3 61.4 + - - +
1110B ILE* 3.5 14.8 + - - +
1113B THR* 3.2 34.2 + - - +
1115B GLN* 4.5 9.5 + - - -
1126B VAL* 4.9 10.5 - - - -
1173B THR* 4.0 9.4 - - - -
1174B THR 3.2 11.9 - - - -
1175B THR* 5.1 5.2 - - - -
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Residues in contact with VAL1103 (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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11A ILE* 5.9 2.5 - - + -
1101B ALA* 4.9 2.2 - - + +
1102B SER* 1.3 76.0 - - - +
1104B CYS* 1.3 73.1 + - - +
1108B GLY 4.5 4.7 - - - +
1109B SER 4.0 5.2 - - - +
1110B ILE* 3.6 29.8 - - + -
1173B THR* 2.7 17.6 + - - -
1174B THR* 2.9 23.6 + - - +
1176B VAL* 3.7 30.5 - - + +
1178B ILE* 5.4 5.8 - - + -
1198B TYR* 4.3 13.9 - - + +
1200B VAL* 3.8 22.8 - - + +
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Residues in contact with CYS1104 (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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1102B SER 4.2 0.6 + - - -
1103B VAL* 1.3 82.0 - - - +
1105B ARG* 1.3 71.2 + - - +
1106B GLU* 3.4 13.5 - - - -
1107B CYS* 2.7 23.3 - - - -
1108B GLY* 3.3 19.7 - - - -
1109B SER 3.2 13.6 + - - +
1112B THR* 5.3 0.2 - - + -
1113B THR* 5.2 2.8 - - - +
1128B CYS* 3.4 16.6 - - + -
1172B GLU 3.4 14.6 - - - -
1173B THR* 3.7 4.2 + - - -
1198B TYR 4.2 1.7 - - - +
1200B VAL* 4.9 2.8 - - - +
1301B ZN 2.3 35.0 - - - -
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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