Contacts of the strand formed by residues 1115 - 1118 (chain B) in PDB entry 2NVU
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 SER1115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1113B ALA 4.7 2.4 + - - -
1114B LEU* 1.3 74.2 - - - +
1116B LEU* 1.3 62.9 + - - +
1117B ILE* 3.8 4.2 + - - +
1227B ILE* 3.3 3.0 - - - +
1228B ASN 2.7 38.8 + - - +
1229B GLY* 4.5 5.2 - - - -
1233B TRP* 4.8 1.0 - - - -
1245B VAL* 3.4 28.0 - - - +
1246B THR 4.2 5.2 - - - -
1248B LEU* 3.4 13.5 - - - -
1320B ALA* 5.6 0.2 - - - -
1321B THR* 5.1 2.6 + - - -
1324B ASN* 3.3 21.8 - - - -
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Residues in contact with LEU1116 (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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1115B SER* 1.3 76.2 - - - +
1117B ILE* 1.3 65.2 + - - +
1118B TYR* 3.8 0.4 - - + +
1127B PRO* 5.3 1.1 - - + -
1130B TRP* 5.7 3.1 - - + -
1133B ILE* 5.4 0.9 - - + -
1148B LEU* 5.1 6.5 - - + -
1225B MET* 3.0 56.5 - - + -
1226B THR 3.8 6.1 - - - +
1227B ILE* 4.4 10.1 - - + -
1244B GLY 3.8 0.2 - - - +
1245B VAL 3.8 1.2 - - - -
1246B THR* 2.8 49.4 + - + +
1247B VAL 3.6 11.4 - - - +
1248B LEU* 3.1 17.2 - - + +
1249B PRO* 3.3 31.4 - - + -
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Residues in contact with ILE1117 (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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1115B SER* 4.6 10.3 - - - +
1116B LEU* 1.3 75.2 - - - +
1118B TYR* 1.3 61.1 + - - +
1218B PHE* 3.5 28.6 - - + -
1225B MET* 3.0 2.3 - - - -
1226B THR* 2.8 44.1 + - + +
1228B ASN* 4.3 19.7 - - + +
1229B GLY 4.8 1.6 - - - +
1232B ALA* 5.7 0.2 - - + -
1233B TRP* 3.1 40.2 - - + +
1236B ILE* 4.4 10.3 - - + -
1243B TYR* 3.5 15.9 - - + -
1244B GLY 3.1 18.6 - - - +
1245B VAL* 4.6 4.0 - - + -
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Residues in contact with TYR1118 (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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1116B LEU* 3.8 1.1 - - + +
1117B ILE* 1.3 76.4 - - - +
1119B ASN* 1.3 62.5 + - - +
1120B LYS* 3.0 41.3 + - - -
1123B LEU* 2.8 33.0 - - + -
1124B PRO* 3.9 7.5 + - + -
1125B ASN 4.4 1.3 - - - -
1126B PRO* 3.0 35.7 - - + +
1218B PHE* 4.1 3.8 - - - -
1224B ALA 2.8 12.1 - - - +
1225B MET* 3.3 32.5 - - + -
1243B TYR* 3.1 16.6 - - - -
1244B GLY* 3.2 17.3 + - - -
1246B THR* 3.3 28.0 - - + -
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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