Contacts of the helix formed by residues 962 - 978 (chain A) in PDB entry 3VF0
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 962 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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961A VAL* 1.3 70.8 - - - +
963A GLN* 1.3 60.9 + - - +
964A PRO* 3.1 13.6 - - - +
965A ILE* 2.9 40.2 + - + +
966A LEU* 3.1 19.1 + - - +
1001A SER* 2.9 16.4 + - - +
1004A VAL* 3.7 22.2 - - + -
1005A ARG* 3.9 6.7 - - - +
1087A THR* 3.4 24.4 - - - +
1088A GLU* 5.2 2.8 + - - -
1091A VAL* 3.5 12.9 - - - +
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Residues in contact with GLN 963 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961A VAL* 3.6 20.2 + - - +
962A ASN* 1.3 69.7 - - - +
964A PRO* 1.4 65.0 - - + +
966A LEU* 3.2 24.0 + - - +
967A ALA* 2.8 38.8 + - + +
970A GLN* 4.8 4.9 + - - -
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Residues in contact with PRO 964 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962A ASN* 3.1 17.0 - - - +
963A GLN* 1.4 91.9 - - + +
965A ILE* 1.4 59.6 + - - +
967A ALA* 4.0 5.6 - - + +
968A ALA* 3.2 23.6 + - - +
1088A GLU* 5.6 3.8 - - - +
1091A VAL* 3.6 29.2 - - + -
1095A GLN* 4.2 14.5 + - - +
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Residues in contact with ILE 965 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
962A ASN* 2.9 30.3 + - - +
964A PRO* 1.4 69.9 - - - +
966A LEU* 1.3 65.3 + - - +
968A ALA* 3.6 6.4 + - - +
969A ALA* 3.2 21.0 + - - +
997A MET* 3.5 41.1 - - - +
1000A MET* 3.8 19.1 - - + -
1001A SER* 3.8 15.3 - - - +
1004A VAL* 4.2 19.5 - - + -
1087A THR* 4.8 1.3 - - + +
1090A LEU* 4.3 2.7 - - + -
1091A VAL* 3.7 35.0 - - + +
1094A ALA* 4.2 6.7 - - + -
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Residues in contact with LEU 966 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961A VAL* 3.9 21.1 - - + -
962A ASN 3.1 17.2 + - - +
963A GLN* 3.7 23.3 - - - +
965A ILE* 1.3 74.5 - - - +
967A ALA* 1.4 58.9 + - - +
969A ALA* 3.1 5.1 + - - +
970A GLN* 2.8 61.9 + - + +
998A ALA* 4.0 22.7 - - + +
1001A SER* 3.6 18.5 - - - +
1002A ARG* 5.7 1.8 - - - +
92B TYR 6.0 0.4 - - - +
93B LYS* 5.4 12.3 - - - +
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Residues in contact with ALA 967 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
963A GLN* 2.8 28.7 + - + +
964A PRO* 4.0 6.5 - - + +
966A LEU* 1.4 72.5 - - - +
968A ALA* 1.3 55.7 + - - +
970A GLN* 3.5 11.9 + - - +
971A SER* 3.0 30.7 + - - -
974A ARG* 4.3 5.6 + - - +
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Residues in contact with ALA 968 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
964A PRO 3.2 18.4 + - - +
965A ILE* 3.7 7.0 - - - +
967A ALA* 1.3 75.7 - - - +
969A ALA* 1.3 59.5 + - - +
971A SER* 3.4 6.9 + - - -
972A LEU 3.2 16.8 + - - -
1094A ALA* 4.4 2.5 - - + +
1095A GLN* 4.2 26.9 - - + +
1098A MET* 3.5 31.3 - - + +
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Residues in contact with ALA 969 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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965A ILE 3.2 13.8 + - - +
966A LEU* 3.1 10.4 + - + +
968A ALA* 1.3 71.3 - - - +
970A GLN* 1.3 60.9 + - + +
972A LEU* 3.2 2.1 + - - -
973A HIS* 2.9 24.7 + - - +
994A ALA* 3.4 32.3 - - - +
997A MET* 3.7 6.5 - - + -
998A ALA* 3.6 22.2 - - + +
1098A MET* 4.1 12.3 - - - +
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Residues in contact with GLN 970 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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963A GLN* 4.8 4.5 + - - -
966A LEU* 2.8 51.1 + - + +
967A ALA* 3.8 8.7 - - - +
969A ALA* 1.3 74.4 - - - +
971A SER* 1.3 54.2 + - - +
973A HIS* 3.3 10.8 + - + +
974A ARG* 2.8 57.6 + - - +
998A ALA* 6.1 0.7 - - + -
93B LYS* 5.7 3.2 - - - +
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Residues in contact with SER 971 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
967A ALA 3.0 18.4 + - - -
968A ALA* 3.6 8.5 - - - -
969A ALA 3.2 0.2 - - - -
970A GLN* 1.3 73.9 - - - +
972A LEU* 1.4 64.0 + - - +
974A ARG* 3.5 24.2 + - - +
975A GLU* 3.2 22.3 + - - +
1102A LYS* 2.8 33.7 + - - +
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Residues in contact with LEU 972 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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968A ALA 3.2 8.5 + - - +
969A ALA 3.2 6.7 + - - +
971A SER* 1.4 76.4 - - - +
973A HIS* 1.3 58.7 + - - +
975A GLU* 3.3 4.6 + - + +
976A ALA* 2.9 28.0 + - + +
990A ALA* 3.4 32.1 - - + +
993A MET* 3.9 9.9 - - + -
994A ALA* 4.0 3.6 - - + +
1098A MET* 3.7 43.3 - - + +
1101A VAL* 3.7 31.6 - - + -
1102A LYS* 3.8 26.2 - - + +
1105A VAL* 5.4 2.2 - - + -
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Residues in contact with HIS 973 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
969A ALA 2.9 16.7 + - - +
970A GLN* 3.5 12.1 - - + +
972A LEU* 1.3 73.4 - - - +
974A ARG* 1.3 65.2 + - + +
976A ALA* 4.7 3.1 - - - -
977A THR* 2.9 63.5 + - + +
991A LYS* 4.9 8.0 + - + +
994A ALA* 3.6 18.4 - - + +
995A LEU* 4.6 12.0 - - + +
92B TYR* 3.4 43.0 + + - -
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Residues in contact with ARG 974 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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967A ALA* 4.3 6.9 + - - +
970A GLN* 2.8 43.2 + - - +
971A SER* 3.5 35.5 + - - +
973A HIS* 1.3 79.4 - - + +
975A GLU* 1.4 61.6 + - - +
977A THR* 3.3 15.2 + - - -
978A LYS* 3.4 19.7 + - - +
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Residues in contact with GLU 975 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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971A SER 3.2 11.2 + - - +
972A LEU* 3.5 9.9 - - + +
974A ARG* 1.4 79.9 - - - +
976A ALA* 1.3 61.4 + - - +
978A LYS* 2.9 51.7 + - - +
979A TRP* 3.4 13.2 + - - -
1102A LYS* 4.0 27.3 - - + +
1105A VAL* 4.7 12.8 - - + +
1106A ARG* 3.1 45.3 + - - +
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Residues in contact with ALA 976 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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972A LEU* 2.9 16.7 + - + +
973A HIS 4.1 2.0 - - - +
975A GLU* 1.3 73.3 - - - +
977A THR* 1.3 57.6 + - - +
978A LYS 3.1 5.2 - - - -
979A TRP* 3.1 24.6 + - - +
987A ILE* 3.5 19.4 - - + +
990A ALA* 4.0 24.5 - - + -
991A LYS* 3.5 30.4 - - + +
1105A VAL* 5.5 2.0 - - + -
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Residues in contact with THR 977 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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973A HIS* 2.9 56.0 + - + +
974A ARG* 3.3 11.3 + - - -
976A ALA* 1.3 71.0 - - - +
978A LYS* 1.3 58.6 + - - +
979A TRP 3.1 6.5 + - - +
991A LYS* 3.8 24.0 - - + +
1128A LYS* 3.3 18.5 - - - +
1129A THR* 5.0 1.6 - - - +
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Residues in contact with LYS 978 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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974A ARG* 3.4 18.1 + - - +
975A GLU* 2.9 47.0 + - - +
976A ALA 3.1 0.8 - - - -
977A THR* 1.3 77.1 - - - +
979A TRP* 1.4 70.8 + - + +
1106A ARG* 5.4 0.2 - - - +
1127A ARG* 3.3 9.2 - - - +
1128A LYS 2.7 26.2 + - - -
1129A THR* 4.0 22.9 + - + +
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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
------------------------------------------------------------
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