Contacts of the strand formed by residues 1423 - 1434 (chain H) 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 PHE1423 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1281H PRO* 4.5 14.6 - - + -
1282H ARG* 3.4 54.3 - - + +
1378H ILE* 3.9 13.2 - - + -
1379H GLU 3.1 24.9 - - - -
1381H VAL* 2.6 74.3 + - + +
1421H ASN 4.4 5.4 - - - -
1422H THR* 1.0 92.0 + - - +
1424H GLN* 1.3 64.1 + - - +
1425H LYS* 4.0 19.7 - - + -
1471H GLU* 6.2 0.7 - - + -
1472H VAL 3.5 12.1 - - - +
1473H THR* 4.5 1.6 - - + -
1474H PHE* 4.2 6.5 - - - -
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Residues in contact with GLN1424 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1380H SER* 3.7 15.5 - - - +
1382H VAL* 4.4 12.9 - - + +
1423H PHE* 1.3 76.4 - - - +
1425H LYS* 1.3 69.5 + - - +
1426H THR* 3.5 29.2 + - + +
1470H THR 3.9 1.6 - - - +
1471H GLU* 3.7 0.6 - - - -
1472H VAL* 2.8 46.4 + - + +
1474H PHE* 3.7 29.2 - - + -
1480H PHE* 6.4 0.7 - - - -
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Residues in contact with LYS1425 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1282H ARG* 5.6 10.7 + - - +
1377H VAL* 5.2 9.5 - - - +
1378H ILE 4.8 4.8 + - - -
1379H GLU* 3.7 46.9 + - + +
1380H SER* 2.9 18.8 + - - -
1423H PHE* 4.0 17.6 - - + -
1424H GLN* 1.3 74.6 - - - +
1426H THR* 1.3 68.3 + - - +
1470H THR 3.8 5.2 - - - +
1471H GLU* 3.3 42.0 + - + +
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Residues in contact with THR1426 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1379H GLU* 5.0 2.0 - - - -
1424H GLN* 3.5 31.0 + - + +
1425H LYS* 1.3 79.9 - - - +
1427H VAL* 1.3 65.7 + - - +
1428H GLU* 3.6 9.4 + - - -
1469H GLU* 3.6 3.3 - - - +
1470H THR* 3.0 48.2 + - - +
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Residues in contact with VAL1427 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1379H GLU* 5.3 8.1 + - - +
1426H THR* 1.3 72.4 - - - +
1428H GLU* 1.3 72.4 + - - +
1429H PRO* 3.6 2.9 - - - +
1468H THR 4.0 3.1 - - - +
1469H GLU* 3.3 35.4 - - + +
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Residues in contact with GLU1428 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1426H THR* 3.6 9.1 + - - -
1427H VAL* 1.3 82.0 - - - +
1429H PRO* 1.3 88.2 - - + +
1430H VAL* 5.2 2.3 - - - +
1431H TYR* 4.0 7.0 + - + -
1467H GLU* 5.1 0.5 - - - -
1468H THR* 2.8 41.1 + - + +
1470H THR* 2.9 36.1 - - + +
1514H ASN* 4.7 0.5 + - - -
1517H VAL* 3.5 28.8 - - + +
1521H LYS* 5.7 0.3 - - - -
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Residues in contact with PRO1429 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1427H VAL* 3.6 3.8 - - + +
1428H GLU* 1.3 106.3 - - + +
1430H VAL* 1.3 66.0 + - + +
1431H TYR* 3.2 36.2 + - + +
1466H PHE 3.7 4.5 - - - +
1468H THR 4.6 0.2 + - - -
1526H THR* 4.1 15.9 - - + -
1527H LEU 4.6 8.1 - - - +
1528H GLU* 6.3 0.7 - - + -
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Residues in contact with VAL1430 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1428H GLU 5.2 1.6 - - - +
1429H PRO* 1.3 75.2 - - + +
1431H TYR* 1.3 62.8 + - - +
1465H THR* 3.9 28.3 - - + -
1466H PHE 3.5 10.1 - - - +
1467H GLU* 3.7 32.8 - - + +
1526H THR* 3.8 3.1 - - - -
1527H LEU* 3.0 47.2 + - + +
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Residues in contact with TYR1431 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1428H GLU* 4.0 12.0 + - + -
1429H PRO* 3.2 40.8 - - + +
1430H VAL* 1.3 73.6 - - - +
1432H GLN* 1.3 61.8 + - - +
1465H THR* 3.2 5.4 - - - -
1466H PHE* 2.8 42.6 + - + -
1468H THR* 5.7 1.8 - - - -
1517H VAL* 3.6 19.0 - - + +
1520H LEU* 3.6 54.5 - - + +
1521H LYS* 3.6 39.3 - - + +
1524H GLY* 5.2 1.1 - - - -
1525H SER 3.4 7.6 - - - +
1526H THR* 3.0 31.4 - - + +
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Residues in contact with GLN1432 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1430H VAL 4.0 1.0 + - - -
1431H TYR* 1.3 71.9 - - - +
1433H MET* 1.3 63.6 + - - +
1434H HIS* 4.4 4.3 + - - +
1463H THR* 3.9 18.7 - - + +
1464H LEU 3.3 9.0 - - - +
1465H THR* 3.9 10.1 - - + +
1492H GLU* 3.9 18.2 - - - +
1524H GLY* 3.5 5.1 - - - -
1525H SER* 2.9 46.9 + - - +
1527H LEU* 3.6 33.6 - - + +
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Residues in contact with MET1433 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1431H TYR* 6.3 0.2 - - + -
1432H GLN* 1.3 76.8 - - - +
1434H HIS* 1.3 60.8 + - - +
1435H ILE* 3.5 16.3 + - + +
1440H ASP* 5.6 6.5 - - + +
1443H VAL* 5.7 1.6 - - + -
1444H LEU* 3.9 23.1 - - + -
1463H THR* 3.5 3.8 - - - -
1464H LEU* 2.7 38.8 + - + +
1466H PHE* 3.7 33.0 - - + -
1519H PHE* 3.8 33.2 - - + -
1520H LEU* 4.4 4.9 - - - -
1523H ASN* 3.3 32.8 - - + +
1524H GLY* 4.9 1.3 - - - -
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Residues in contact with HIS1434 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1432H GLN* 5.6 4.2 + - - +
1433H MET* 1.3 74.7 - - - +
1435H ILE* 1.3 61.0 + - - +
1436H LYS* 2.9 29.4 + - + +
1440H ASP* 4.2 4.2 - - - +
1461H ASN 5.8 2.9 - - - -
1462H LYS 4.0 6.7 - - - -
1463H THR* 3.6 30.9 + - + +
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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