Contacts of the strand formed by residues 994 - 1007 (chain A) in PDB entry 1VDV
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 LYS 994 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544A SER* 3.1 47.6 + - - +
545A ALA* 5.2 2.4 - - - +
547A LEU* 5.0 7.0 + - - -
987A PHE* 3.7 17.9 - - + -
991A ASN* 3.3 19.6 - - + +
992A CYS 3.6 1.0 - - - -
993A TRP* 1.3 83.4 - - + +
995A LYS* 1.3 75.1 + - - +
1163A GLU* 3.6 22.7 - - + +
1164A ILE 3.3 12.8 - - - +
1165A ASP* 3.3 18.9 + - - -
1166A CYS* 3.7 0.9 - - - -
5001A GOL 2.8 35.1 + - - +
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Residues in contact with LYS 995 (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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987A PHE* 4.1 1.1 - - - -
988A ASN* 2.7 45.4 + - + +
991A ASN 2.7 16.2 + - - +
992A CYS 4.1 8.1 - - - -
994A LYS* 1.3 84.5 - - - +
996A ARG* 1.3 65.1 + - - +
1163A GLU* 3.3 2.8 - - - -
1164A ILE* 2.8 38.7 + - + +
1166A CYS* 3.6 15.4 - - - -
1277A ALA* 3.5 19.4 - - - +
1280A ALA* 3.9 20.6 + - + -
1281A ALA* 3.8 14.4 - - - +
1284A GLN* 2.9 29.8 - - - +
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Residues in contact with ARG 996 (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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983A GLU* 3.3 23.4 + - - -
984A VAL* 3.3 22.1 - - + +
987A PHE* 3.4 42.4 - - + -
988A ASN* 2.8 25.9 + - - +
995A LYS* 1.3 76.5 - - - +
997A GLY* 1.3 59.5 + - - +
1161A GLU* 3.7 15.3 + - - +
1162A VAL 3.1 13.0 - - - +
1163A GLU* 3.0 27.7 + - + -
1174A LEU* 3.6 27.4 - - - +
1276A ASP* 4.3 2.1 - - - +
1277A ALA* 3.7 11.8 + - - -
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Residues in contact with GLY 997 (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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984A VAL* 4.4 2.5 - - - -
996A ARG* 1.3 76.8 - - - +
998A LEU* 1.3 60.5 + - - -
1161A GLU* 3.1 10.0 - - - +
1162A VAL 3.0 29.0 + - - -
1273A ALA* 3.3 26.6 - - - +
1276A ASP* 3.4 9.2 - - - -
1277A ALA* 3.8 4.6 - - - +
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Residues in contact with LEU 998 (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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977A TYR* 3.5 51.7 + - + +
980A ARG* 4.1 17.0 - - + +
981A LYS* 3.8 25.4 - - + +
984A VAL* 4.2 12.3 - - + +
997A GLY* 1.3 74.1 - - - -
999A CYS* 1.3 64.5 + - - +
1159A CYS* 3.6 23.8 - - - -
1160A SER 3.4 9.0 - - - +
1161A GLU* 3.8 19.7 - - + +
1273A ALA* 4.1 1.3 - - - +
1276A ASP* 3.2 19.1 + - - +
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Residues in contact with CYS 999 (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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938A ALA* 6.0 1.6 - - - -
942A ARG* 4.1 11.9 - - - -
977A TYR* 4.6 4.5 - - - -
998A LEU* 1.3 78.4 - - - +
1000A ILE* 1.3 62.4 + - - +
1001A ILE* 3.5 25.8 - - - -
1158A ALA 3.7 1.6 - - - +
1159A CYS* 3.2 4.2 - - - -
1160A SER 2.9 31.9 + - - -
1269A SER* 3.9 8.8 - - - +
1272A PHE* 3.5 26.5 - - - +
1273A ALA* 3.8 20.9 - - - +
1276A ASP* 5.6 0.2 - - + -
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Residues in contact with ILE1000 (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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939A GLU* 3.9 15.5 - - + -
942A ARG* 3.9 7.8 + - - +
968A TRP* 3.6 32.6 - - + +
971A CYS* 4.0 15.9 - - + -
972A LEU* 3.6 31.2 - - + +
977A TYR* 3.9 21.9 + - + +
999A CYS* 1.3 74.3 - - - +
1001A ILE* 1.3 72.5 + - - +
1157A VAL* 3.6 28.7 - - + -
1158A ALA 3.3 6.5 - - - +
1159A CYS* 4.0 12.6 - - + +
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Residues in contact with ILE1001 (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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924A GLU* 3.7 21.5 - - + +
942A ARG* 3.2 44.0 - - - +
968A TRP* 4.3 0.2 - - - -
999A CYS* 3.5 18.2 - - - -
1000A ILE* 1.3 78.7 - - - +
1002A PRO* 1.3 82.1 - - + +
1157A VAL* 3.3 5.5 - - - +
1158A ALA 2.8 36.7 + - - +
1265A PHE* 4.0 12.1 - - + +
1266A LEU* 3.7 8.3 - - + +
1268A ALA* 5.6 0.7 - - + -
1269A SER* 4.2 22.2 - - - +
1272A PHE* 4.6 8.3 - - + -
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Residues in contact with PRO1002 (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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887A ASN* 3.4 11.2 + - - +
888A CYS* 4.2 9.6 - - + -
889A TYR* 3.4 31.4 - - + +
924A GLU* 3.8 0.2 - - - +
942A ARG* 4.3 1.8 - - - -
946A MET* 4.3 4.5 - - + -
964A VAL* 3.9 24.5 - - + -
968A TRP* 3.7 17.7 - - + -
1001A ILE* 1.3 108.3 - - + +
1003A THR* 1.3 65.7 + - - +
1156A GLY 3.4 7.9 - - - +
1157A VAL* 3.9 9.9 - - + -
1265A PHE* 4.2 0.9 - - - -
1266A LEU* 4.3 0.9 - - - -
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Residues in contact with THR1003 (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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887A ASN* 3.3 8.5 + - - -
888A CYS* 3.4 6.8 - - - -
920A LEU* 3.6 25.1 - - - +
964A VAL* 4.3 0.9 - - - +
1002A PRO* 1.3 80.7 - - - +
1004A LYS* 1.3 70.1 + - - +
1005A PHE* 5.7 0.5 - - - +
1154A THR 5.3 0.4 - - - +
1155A TYR* 3.5 6.2 - - - +
1156A GLY 3.0 31.6 + - - +
1180A MET* 4.7 3.8 - - + -
1262A PRO* 3.8 21.6 + - + +
1265A PHE* 3.6 11.4 - - + +
1266A LEU* 3.6 26.2 - - + +
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Residues in contact with LYS1004 (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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883A PHE 4.3 8.6 + - - -
884A HIS* 3.4 17.8 - - + +
886A ASP* 2.7 31.8 + - - -
887A ASN* 2.6 33.5 + - - +
888A CYS* 3.7 7.2 - - - -
920A LEU* 4.4 6.6 - - - +
947A TYR* 4.3 4.7 - - + -
953A THR* 4.2 13.9 - - - +
955A PHE* 5.3 0.2 - - - -
959A LEU* 4.4 6.5 - - + -
962A PHE* 4.6 7.4 - - + -
1003A THR* 1.3 82.2 + - - +
1005A PHE* 1.3 62.5 + - - +
1153A PHE* 3.9 29.2 - - + -
1154A THR 3.4 7.2 - - - -
1155A TYR* 3.4 27.6 - - + -
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Residues in contact with PHE1005 (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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880A ARG* 3.4 29.4 - - - -
884A HIS* 3.6 10.5 - + - -
913A GLY* 3.6 31.2 - - - -
916A GLY* 4.6 7.0 - - - -
917A PRO* 5.0 2.0 - - + -
920A LEU* 5.1 8.7 - - + -
1003A THR* 5.7 0.7 - - + +
1004A LYS* 1.3 75.8 - - - +
1006A GLY* 1.3 72.5 + - - +
1007A ILE* 3.4 18.8 + - + +
1079A ALA 5.4 2.2 - - - -
1080A SER* 4.8 0.4 - - - -
1153A PHE* 3.3 6.2 - - - -
1154A THR 3.0 29.5 + - - +
1261A GLU* 3.7 36.1 - - + -
1262A PRO* 3.7 37.7 - - + +
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Residues in contact with GLY1006 (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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880A ARG* 2.9 27.4 + - - -
884A HIS* 2.9 14.8 + - - -
1005A PHE* 1.3 78.0 - - - +
1007A ILE* 1.3 57.4 + - - -
1150A PHE* 3.3 31.7 - - - -
1153A PHE* 3.6 17.0 - - - -
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Residues in contact with ILE1007 (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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1005A PHE* 3.6 35.9 - - + +
1006A GLY* 1.3 70.8 - - - +
1008A SER* 1.3 72.9 + - - +
1079A ALA 4.6 1.3 - - - +
1080A SER* 4.8 3.6 - - - -
1081A VAL* 3.3 26.7 - - + -
1084A ASP* 4.1 1.8 - - - +
1150A PHE* 3.5 2.5 - - - +
1151A HIS* 3.0 18.5 + - + +
1152A TYR* 2.9 41.9 + - + +
1154A THR* 3.6 21.5 - - - +
1258A ALA* 3.8 27.4 - - + -
1262A PRO* 4.0 7.0 - - + -
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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