Contacts of the helix formed by residues 1443 - 1460 (chain A) in PDB entry 2YVI
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 SER1443 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1440A ASN 3.7 3.0 + - - +
1441A PRO 3.6 3.0 + - - -
1442A ASN* 1.3 82.1 - - - +
1444A LEU* 1.3 64.1 + - - +
1445A LEU* 3.2 11.8 + - - +
1446A GLU* 2.9 48.2 + - - +
1447A GLN* 3.1 29.9 + - - +
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Residues in contact with LEU1444 (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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1416A GLY* 3.9 21.8 - - - +
1417A LEU* 3.8 43.1 - - + +
1419A TRP* 3.9 12.0 - - + +
1443A SER* 1.3 72.9 + - - +
1445A LEU* 1.3 57.7 + - - +
1447A GLN* 3.4 22.1 + - - +
1448A SER* 2.8 35.0 + - - -
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Residues in contact with LEU1445 (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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1412A SER* 3.5 30.5 - - - +
1413A GLU* 3.7 39.5 - - - +
1443A SER* 3.1 8.4 - - - +
1444A LEU* 1.3 79.7 - - - +
1446A GLU* 1.3 60.6 + - + +
1448A SER* 3.1 4.7 + - - -
1449A VAL* 2.9 41.6 + - + +
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Residues in contact with GLU1446 (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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1439A GLU 5.2 0.3 - - - +
1440A ASN* 3.8 32.3 - - + +
1442A ASN 5.4 0.7 + - - -
1443A SER* 2.9 34.0 + - - +
1445A LEU* 1.3 80.0 - - + +
1447A GLN* 1.3 56.6 + - - +
1449A VAL* 3.4 7.7 + - - +
1450A ALA* 2.9 30.0 + - - +
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Residues in contact with GLN1447 (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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1419A TRP* 2.8 51.8 + - + +
1436A ILE* 3.5 23.8 - - + +
1437A ARG* 4.3 9.1 + - - +
1440A ASN* 2.6 37.3 + - + +
1441A PRO* 3.8 15.2 + - - +
1443A SER 3.1 16.9 + - - +
1444A LEU* 3.6 14.9 - - - +
1446A GLU* 1.3 77.7 - - - +
1448A SER* 1.3 58.1 + - - +
1450A ALA 3.4 0.7 + - - -
1451A LEU* 3.0 26.7 + - - +
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Residues in contact with SER1448 (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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1412A SER* 3.5 31.4 + - - -
1415A LEU* 3.7 17.5 - - - +
1416A GLY 4.1 3.6 + - - -
1419A TRP* 3.5 24.9 - - - +
1444A LEU 2.8 22.5 + - - -
1445A LEU 3.5 1.8 - - - -
1447A GLN* 1.3 74.1 - - - +
1449A VAL* 1.3 65.5 + - - +
1451A LEU* 3.2 4.2 + - - +
1452A LEU* 3.1 27.2 + - - +
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Residues in contact with VAL1449 (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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1412A SER* 3.6 24.9 - - - +
1445A LEU* 2.9 32.9 + - + +
1446A GLU* 3.8 6.5 - - - +
1448A SER* 1.3 75.2 - - - +
1450A ALA* 1.3 63.1 + - - +
1452A LEU* 3.3 4.3 + - - +
1453A ASN* 3.0 25.1 + - + +
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Residues in contact with ALA1450 (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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1436A ILE* 4.0 13.3 - - + +
1440A ASN* 3.8 20.4 - - - +
1446A GLU 2.9 18.6 + - - +
1447A GLN 3.6 4.9 - - - +
1448A SER 3.2 0.2 - - - -
1449A VAL* 1.3 78.8 - - - +
1451A LEU* 1.3 57.1 + - - +
1453A ASN* 3.3 9.2 + - - +
1454A LEU* 3.0 28.4 + - - +
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Residues in contact with LEU1451 (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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1415A LEU* 5.3 1.8 - - + -
1419A TRP* 4.2 13.9 - - + +
1422A LEU* 4.3 9.4 - - + -
1423A ALA* 3.7 29.8 - - + -
1426A LEU* 4.3 18.2 - - + -
1428A PHE* 3.9 24.2 - - + -
1436A ILE* 3.9 21.0 - - + +
1447A GLN 3.0 14.6 + - - +
1448A SER* 3.2 8.9 + - - +
1450A ALA* 1.3 77.5 - - - +
1452A LEU* 1.3 78.7 + - + +
1454A LEU* 3.1 3.5 + - + +
1455A TRP* 3.0 25.1 + - + +
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Residues in contact with LEU1452 (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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1408A MET* 3.3 45.5 - - + +
1411A ILE* 3.9 12.3 - - + -
1412A SER* 3.8 22.4 - - - +
1415A LEU* 4.9 2.2 - - + -
1422A LEU* 4.6 8.1 - - + -
1448A SER 3.1 12.2 + - - +
1449A VAL* 3.9 4.0 - - - +
1451A LEU* 1.3 92.1 - - + +
1453A ASN* 1.3 57.4 + - - +
1455A TRP* 3.3 5.9 + - + +
1456A VAL* 3.0 33.9 + - - +
1468A LEU* 4.1 32.3 - - + -
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Residues in contact with ASN1453 (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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1449A VAL* 3.0 20.5 + - + +
1450A ALA* 3.5 8.7 + - - +
1451A LEU 3.2 0.2 - - - -
1452A LEU* 1.3 79.3 - - - +
1454A LEU* 1.3 63.2 + - - +
1456A VAL* 3.4 9.5 + - - +
1457A ILE* 3.2 43.5 + - - +
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Residues in contact with LEU1454 (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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1428A PHE* 3.5 30.7 - - + -
1432A ASP* 4.3 22.0 - - + +
1436A ILE* 4.3 20.9 - - + -
1450A ALA 3.0 13.2 + - - +
1451A LEU* 3.1 9.4 + - + +
1453A ASN* 1.3 79.8 - - - +
1455A TRP* 1.3 56.2 + - - +
1457A ILE* 3.4 15.1 + - + +
1458A ARG* 2.9 29.9 + - + +
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Residues in contact with TRP1455 (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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1408A MET* 4.1 13.5 - - - -
1426A LEU* 4.2 21.7 - - + +
1428A PHE* 3.7 13.9 - + + -
1451A LEU* 3.0 15.7 + - + +
1452A LEU* 3.6 9.9 - - + +
1453A ASN 3.2 0.2 - - - -
1454A LEU* 1.3 76.0 - - - +
1456A VAL* 1.3 86.6 + - + +
1458A ARG* 3.2 25.2 + - - +
1459A GLU* 2.9 57.5 + - + +
1463A ALA* 4.3 10.1 - - + -
1464A ASN 3.7 39.0 - - - -
1465A MET* 4.2 6.5 - - - -
1467A ASN* 4.6 9.8 - - + +
1468A LEU* 3.5 44.0 - - + -
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Residues in contact with VAL1456 (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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1408A MET* 3.4 36.3 - - + -
1452A LEU 3.0 22.0 + - - +
1453A ASN* 3.4 10.3 + - - +
1455A TRP* 1.3 83.4 - - + +
1457A ILE* 1.3 61.3 + - + +
1459A GLU* 4.3 1.7 - - - +
1460A GLY* 3.0 28.8 + - - +
1463A ALA* 5.1 2.9 - - - +
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Residues in contact with ILE1457 (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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1453A ASN* 3.2 38.0 + - - +
1454A LEU* 3.7 16.4 - - + +
1456A VAL* 1.3 82.8 - - + +
1458A ARG* 1.3 63.7 + - - +
1460A GLY* 3.5 7.8 + - - -
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Residues in contact with ARG1458 (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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1426A LEU* 2.9 32.3 + - - +
1427A GLN* 3.8 17.0 + - - +
1428A PHE* 3.7 30.1 - - + +
1454A LEU* 2.9 19.4 + - + +
1455A TRP* 3.6 22.1 - - - +
1457A ILE* 1.3 80.9 - - - +
1459A GLU* 1.3 85.0 + - - +
1460A GLY 3.6 0.2 + - - -
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Residues in contact with GLU1459 (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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1455A TRP* 2.9 51.8 + - + +
1458A ARG* 1.3 112.1 + - - +
1460A GLY* 1.3 66.5 + - - +
1461A GLN 3.2 0.3 + - - -
1462A ASN* 2.9 36.1 + - - +
1463A ALA* 3.5 23.6 + - + -
1467A ASN* 4.8 9.2 + - - -
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Residues in contact with GLY1460 (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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1456A VAL 3.0 17.9 + - - +
1457A ILE* 3.5 6.7 + - - -
1458A ARG 3.4 2.6 - - - -
1459A GLU* 1.3 77.2 - - - +
1461A GLN* 1.3 61.3 + - - -
1463A ALA* 3.3 16.5 + - - +
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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