Contacts of the strand formed by residues 946 - 957 (chain B) in PDB entry 2NVX
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 ASN 946 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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905B VAL* 3.6 14.8 - - - +
906B SER* 4.1 14.4 - - - +
941B LEU* 4.0 2.9 - - - +
944B THR 5.0 3.0 - - - +
945B GLU* 1.3 87.1 - - - +
947B GLY* 1.3 54.4 + - - +
968B VAL* 4.8 4.8 - - - +
970B THR* 2.6 44.1 + - - +
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Residues in contact with GLY 947 (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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904B ARG* 3.7 7.7 - - - +
905B VAL* 2.7 49.7 + - - +
946B ASN* 1.3 78.9 - - - +
948B ILE* 1.3 61.4 + - - -
968B VAL* 4.4 1.1 - - - -
969B ARG 3.7 6.7 - - - -
970B THR* 4.1 8.3 - - - -
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Residues in contact with ILE 948 (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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901B PRO 4.2 0.7 - - - +
902B GLY* 3.8 9.9 - - - +
903B VAL 3.2 23.6 - - - +
904B ARG* 3.8 24.7 - - + +
947B GLY* 1.3 78.1 - - - -
949B VAL* 1.3 67.2 - - - +
968B VAL* 3.8 3.3 - - - +
969B ARG* 2.6 58.7 + - - +
970B THR* 5.9 0.2 - - - -
60C ASP* 5.1 7.4 - - + +
61C GLU* 3.2 29.4 - - - +
65L VAL* 5.2 2.2 - - + -
67L PHE* 3.5 35.2 - - + -
68L GLU* 5.9 0.2 - - - +
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Residues in contact with VAL 949 (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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899B ILE* 3.8 27.1 - - + -
900B ALA 3.8 13.2 - - - +
901B PRO* 2.6 41.8 - - + +
903B VAL 3.6 6.5 + - - +
905B VAL* 3.8 17.5 - - + -
948B ILE* 1.3 78.7 - - - +
950B ASP* 1.3 63.0 + - - +
951B GLN 4.4 1.3 - - - +
952B VAL* 3.8 23.8 - - + -
966B VAL* 4.1 8.1 - - + -
967B ARG 3.8 10.3 - - - +
968B VAL* 4.2 5.4 - - + +
969B ARG* 4.5 2.8 + - - -
60C ASP* 5.3 2.3 - - - +
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Residues in contact with ASP 950 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
786B ASN* 4.3 2.3 - - - +
856B PHE* 3.8 9.5 - - + -
901B PRO* 3.9 12.0 - - - +
948B ILE 3.5 1.0 + - - -
949B VAL* 1.3 76.2 - - - +
951B GLN* 1.3 67.8 + - - +
967B ARG* 2.3 62.8 + - + +
969B ARG* 2.6 47.0 + - + +
60C ASP* 5.2 0.5 - - - +
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Residues in contact with GLN 951 (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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786B ASN* 3.6 25.3 + - - +
787B VAL* 5.1 4.2 - - - +
789B MET* 4.2 8.0 - - - +
901B PRO* 4.9 4.3 - - + -
949B VAL* 4.8 0.4 - - - -
950B ASP* 1.3 87.0 + - - +
952B VAL* 1.3 67.8 + - - +
953B LEU 4.3 0.2 - - - -
965B LYS 4.1 0.7 - - - +
967B ARG* 3.0 61.7 + - + +
57L LEU* 3.7 33.6 - - + +
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Residues in contact with VAL 952 (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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898B LEU* 4.2 27.4 - - + -
899B ILE* 3.8 21.3 - - + +
901B PRO* 4.6 9.7 - - + +
949B VAL* 3.8 10.5 - - + -
951B GLN* 1.3 82.2 - - - +
953B LEU* 1.3 67.9 + - - +
954B VAL* 4.0 1.1 + - + -
964B VAL* 4.6 6.1 - - + -
965B LYS 3.8 4.3 - - - +
966B VAL* 3.6 25.4 - - + -
57L LEU* 3.1 9.2 - - - +
58L LYS* 3.0 44.3 + - + +
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Residues in contact with LEU 953 (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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119B LEU* 3.7 55.6 - - + +
789B MET* 3.9 8.1 - - + -
952B VAL* 1.3 74.4 - - - +
954B VAL* 1.3 61.5 + - - +
955B THR* 3.5 20.0 - - - +
963B PHE* 5.3 2.0 - - + -
964B VAL* 3.2 10.6 - - - +
965B LYS* 2.9 56.6 + - + +
32L ALA* 5.6 0.7 - - + -
55L ILE* 4.2 11.9 - - + +
56L LEU 3.8 6.7 - - - +
57L LEU* 3.6 25.4 - - + -
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Residues in contact with VAL 954 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898B LEU* 3.7 29.2 - - + -
952B VAL* 4.5 6.7 - - + +
953B LEU* 1.3 75.5 - - - +
955B THR* 1.3 57.6 + - - +
962B LYS* 4.5 18.6 - - + -
963B PHE 3.5 8.3 - - - +
964B VAL* 4.4 9.4 - - + -
29L TYR* 3.8 30.3 - - + +
46L VAL* 3.7 12.6 - - + +
55L ILE 2.4 22.3 - - - +
56L LEU* 2.9 20.8 + - + +
58L LYS* 5.1 0.7 - - + -
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Residues in contact with THR 955 (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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120B ARG* 3.7 26.4 - - + +
953B LEU* 3.5 21.7 - - - +
954B VAL* 1.3 73.0 - - - +
956B THR* 1.3 78.3 + - - +
961B LEU 3.7 0.2 - - - +
962B LYS* 3.8 2.9 - - - -
963B PHE* 2.8 47.1 + - - +
46L VAL* 3.7 10.8 - - - +
54L ARG* 3.1 28.7 - - + +
55L ILE* 3.0 14.4 + - - +
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Residues in contact with THR 956 (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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120B ARG* 3.6 27.6 + - - +
955B THR* 1.3 86.0 - - - +
957B ASN* 1.3 63.0 + - - +
960B GLY* 3.5 10.7 - - - -
961B LEU 3.0 27.5 + - - -
963B PHE* 3.9 5.6 - - - +
46L VAL* 4.1 22.7 - - + +
54L ARG* 4.1 31.0 - - + -
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Residues in contact with ASN 957 (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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104B GLU* 5.8 0.6 - - - +
120B ARG* 3.2 25.0 - - - +
121B ASN* 3.3 15.9 - - - +
122B LEU* 3.5 7.0 - - - +
862B GLN* 4.4 14.7 - - - +
956B THR* 1.3 76.4 + - - +
958B GLN* 1.3 81.1 + - - +
959B ASP* 2.6 11.5 + - - +
960B GLY* 2.5 33.3 + - - -
961B LEU* 3.2 30.9 + - + +
963B PHE* 4.4 6.9 - - + +
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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