Contacts of the strand formed by residues 1019 - 1027 (chain A) in PDB entry 2VKZ
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 ILE1019 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1017A ARG* 4.0 1.8 + - - +
1018A VAL* 1.3 76.5 - - - +
1020A VAL* 1.3 57.2 + - - +
1316A VAL* 3.8 40.8 - - + +
1319A ILE* 3.7 36.8 - - + -
1320A LEU* 4.0 22.9 - - + -
1387A ILE* 3.8 26.5 - - + -
1388A MET 3.6 4.9 - - - +
1389A GLN* 5.1 1.6 - - + -
1403A ILE* 3.6 6.8 - - - +
1404A VAL* 2.8 49.3 + - + +
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Residues in contact with VAL1020 (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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1018A VAL* 4.2 3.4 - - + -
1019A ILE* 1.3 78.2 - - - +
1021A VAL* 1.3 72.2 + - - +
1022A THR* 3.8 7.0 + - - +
1387A ILE* 3.3 4.6 - - - -
1388A MET* 3.0 35.4 + - - +
1390A ALA* 4.1 25.8 - - + -
1393A ALA* 4.5 5.8 - - + -
1400A ILE* 3.4 42.6 - - + -
1402A GLY 3.4 11.7 - - - +
1403A ILE* 4.0 15.5 - - + -
1661A LEU* 4.6 4.7 - - + -
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Residues in contact with VAL1021 (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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1020A VAL* 1.3 71.7 - - - +
1022A THR* 1.3 61.4 + - - +
1023A GLY 3.6 20.4 - - - +
1385A GLN* 4.2 8.3 - - + -
1386A ILE 3.6 4.9 - - - +
1387A ILE* 3.6 20.9 - - + -
1400A ILE* 3.7 3.6 - - - -
1401A TYR* 2.8 31.2 + - + +
1402A GLY 3.0 13.7 + - - +
1404A VAL* 3.6 19.3 - - + +
1593A MET* 3.6 18.6 - - + -
1597A LEU* 3.3 32.3 - - + -
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Residues in contact with THR1022 (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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1020A VAL* 4.3 2.4 - - - +
1021A VAL* 1.3 74.9 - - - +
1023A GLY* 1.3 58.5 + - - +
1226A SER* 2.7 42.6 - - - +
1386A ILE* 2.8 17.7 + - + -
1388A MET* 3.4 42.7 - - + +
1393A ALA* 4.2 4.5 - - - +
1398A VAL* 3.5 19.5 - - + +
1399A PRO* 3.6 11.6 + - - +
1401A TYR* 3.2 18.9 - - - -
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Residues in contact with GLY1023 (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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1021A VAL* 3.6 4.6 - - - +
1022A THR* 1.3 81.8 - - - +
1024A PHE* 1.3 69.0 + - - +
1222A ALA* 3.8 17.5 - - - -
1225A ALA* 4.1 2.5 - - - -
1226A SER* 3.8 4.2 - - - -
1385A GLN* 3.3 4.5 - - - +
1386A ILE* 2.9 26.4 + - - +
1401A TYR* 4.0 9.2 - - - -
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Residues in contact with PHE1024 (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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1023A GLY* 1.3 77.3 - - - +
1025A ALA* 1.3 65.0 + - - +
1033A ALA* 3.9 13.7 - - + +
1221A GLU 4.2 0.2 - - - +
1222A ALA* 3.8 6.8 + - - -
1225A ALA* 3.4 21.9 - - + +
1384A ILE 3.4 11.0 - - - +
1385A GLN* 3.8 7.4 - - + -
1401A TYR* 3.8 36.8 - + - -
1594A ASN* 3.2 40.6 - - + +
1597A LEU* 3.6 24.5 - - + -
1598A GLN* 3.7 38.4 - - + -
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Residues in contact with ALA1025 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1024A PHE* 1.3 78.1 - - - +
1026A GLU* 1.3 65.0 + - - +
1033A ALA* 4.2 9.9 - - - -
1218A SER* 3.5 14.6 - - - +
1221A GLU* 3.5 21.8 - - + +
1222A ALA* 3.4 24.0 - - + +
1384A ILE 3.1 28.9 + - - +
1594A ASN* 3.5 7.1 + - - -
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Residues in contact with GLU1026 (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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1025A ALA* 1.3 78.6 - - - +
1027A VAL* 1.3 67.2 + - - +
1028A GLY* 4.1 4.1 - - - +
1031A GLY 3.8 0.6 - - - +
1032A SER* 3.4 27.2 - - - -
1033A ALA* 3.3 24.9 - - - +
1036A ARG* 2.6 52.3 + - - +
1218A SER* 4.2 3.8 - - - -
1221A GLU* 4.1 4.3 - - - +
1382A ALA 3.4 13.5 - - - +
1383A GLY* 4.1 0.7 - - - -
1581A THR* 5.4 0.2 - - - +
1591A TRP* 3.7 31.7 + - + +
1594A ASN* 3.2 19.8 + - - +
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Residues in contact with VAL1027 (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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1026A GLU* 1.3 77.4 - - - +
1028A GLY* 1.3 60.0 + - - +
1031A GLY 3.8 3.6 - - - +
1189A ILE* 3.8 15.3 - - + -
1193A TRP* 3.6 34.3 - - + +
1198A TYR* 6.1 0.4 - - + -
1214A PHE* 3.6 39.3 - - + +
1217A VAL* 4.1 23.8 - - + -
1218A SER* 3.7 7.4 + - - +
1221A GLU* 6.0 0.7 - - - +
1381A GLY* 3.1 5.5 - - - -
1382A ALA 2.9 30.9 + - - +
1591A TRP* 3.5 2.9 - - - -
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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