Contacts of the strand formed by residues 1515 - 1521 (chain B) in PDB entry 3RYT
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 GLU1515 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1504B ASN* 3.7 32.5 + - + +
1505B CYS 3.8 8.7 - - - +
1506B VAL* 4.7 7.4 - - + +
1514B PRO* 1.3 76.3 - - - +
1516B VAL* 1.3 64.7 + - - +
1517B PRO* 3.9 6.1 - - - +
1595B SER* 6.1 1.1 - - - -
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Residues in contact with VAL1516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1503B LEU 3.6 0.2 - - - +
1504B ASN* 4.1 2.7 - - - -
1505B CYS* 2.8 46.1 + - + +
1506B VAL 5.1 2.2 - - - +
1507B ASN* 5.3 7.4 - - + +
1514B PRO 4.9 5.2 - - - +
1515B GLU* 1.3 74.8 - - - +
1517B PRO* 1.3 70.6 - - + +
1518B VAL* 3.7 5.6 + - + +
1536B ALA* 5.3 4.0 - - + +
1537B VAL* 4.1 30.3 - - + +
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Residues in contact with PRO1517 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1502B THR* 4.2 10.8 - - - +
1503B LEU 3.8 0.7 - - - +
1504B ASN* 3.6 21.1 - - - +
1515B GLU 3.9 6.3 - - - +
1516B VAL* 1.3 91.2 - - + +
1518B VAL* 1.3 63.7 + - - +
1519B LYS 4.1 1.5 + - - +
1536B ALA* 4.8 3.6 - - - +
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Residues in contact with VAL1518 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1502B THR* 3.8 4.1 + - - -
1503B LEU* 3.1 33.6 + - + +
1505B CYS* 4.3 15.7 - - + -
1516B VAL* 3.9 13.0 - - + +
1517B PRO* 1.3 79.9 - - - +
1519B LYS* 1.3 72.4 + - - +
1520B GLY* 3.7 1.2 + - - -
1529B VAL* 6.6 0.4 - - + -
1532B LYS* 3.3 33.9 - - + +
1533B LEU* 4.3 7.9 - - + +
1536B ALA* 3.4 23.1 - - + -
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Residues in contact with LYS1519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1500B THR* 5.5 4.7 - - + -
1501B LEU 3.9 7.0 - - - +
1502B THR* 4.7 6.0 + - - +
1517B PRO* 4.1 1.2 + - - +
1518B VAL* 1.3 84.8 - - - +
1520B GLY* 1.3 59.9 + - - +
1532B LYS* 4.2 9.9 + - - +
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Residues in contact with GLY1520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1500B THR* 3.1 12.7 - - - +
1501B LEU* 2.8 31.7 + - - +
1518B VAL 3.7 0.6 + - - -
1519B LYS* 1.3 76.3 - - - +
1521B LEU* 1.3 70.1 + - - +
1524B ASP* 4.4 1.3 - - - -
1532B LYS* 4.1 15.5 - - - -
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Residues in contact with LEU1521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1471B GLU 3.8 19.1 - - - +
1472B LYS* 4.3 8.5 - - - +
1473B GLY* 3.8 4.3 - - - -
1474B PRO* 3.5 36.3 - - + -
1498B TYR* 3.4 33.9 - - + -
1499B LYS 3.5 9.2 - - - +
1500B THR* 4.4 9.9 - - + +
1501B LEU* 4.0 12.0 - - - +
1520B GLY* 1.3 85.2 - - - +
1522B ASN* 1.3 63.2 + - - +
1523B CYS* 3.6 7.4 - - - +
1524B ASP* 3.5 28.1 + - - +
1529B VAL* 5.6 1.6 - - - +
1532B LYS* 4.4 1.8 - - - +
1585B LEU* 5.0 3.6 - - - +
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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