Contacts of the strand formed by residues 1359 - 1364 (chain C) in PDB entry 3B13
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 LYS1359 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1345C VAL 3.8 0.7 - - - +
1346C GLY* 3.6 1.9 - - - -
1347C TYR* 3.1 26.4 + - - +
1348C TYR* 5.0 0.6 - - - -
1354C SER 3.6 17.2 + - - -
1355C PHE* 3.2 32.5 + - - +
1356C LEU 3.1 9.4 + - - +
1357C ARG 3.4 12.1 - - - +
1358C ASN* 1.3 78.7 - - - +
1360C VAL* 1.3 67.5 + - - +
1361C PHE* 3.8 11.3 - - + -
1483C GLU* 2.8 38.4 + - + +
1484C VAL 5.8 0.2 - - - +
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Residues in contact with VAL1360 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1344C ALA* 4.3 11.2 - - + -
1345C VAL 3.3 17.0 - - - +
1346C GLY* 4.1 4.5 - - - +
1348C TYR* 3.5 23.8 - - + +
1359C LYS* 1.3 78.7 - - - +
1361C PHE* 1.3 74.3 + - - +
1407C GLN* 5.4 1.6 - - - +
1409C PHE* 5.9 2.5 - - + -
1469C PHE* 4.7 10.1 - - + -
1483C GLU* 3.6 2.4 - - - +
1484C VAL* 2.7 52.5 + - + +
1487C MET* 4.4 16.6 - - + -
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Residues in contact with PHE1361 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1343C PHE 3.6 0.9 - - - +
1344C ALA* 3.4 4.9 - - - -
1345C VAL* 2.9 32.6 + - - +
1347C TYR* 3.7 33.9 - + - -
1355C PHE* 3.6 22.4 - + - -
1356C LEU* 4.0 15.5 - - + -
1359C LYS* 3.8 25.6 - - + -
1360C VAL* 1.3 77.6 - - - +
1362C ILE* 1.3 65.2 + - - +
1363C TYR* 4.0 20.4 - + + -
1481C TRP* 4.3 18.2 - + + -
1482C PHE 3.3 7.9 - - - +
1483C GLU* 3.4 36.8 - - + -
1484C VAL* 4.2 0.4 - - - -
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Residues in contact with ILE1362 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1342C TYR* 4.2 6.7 - - + -
1343C PHE 3.5 6.1 - - - +
1344C ALA* 4.0 20.4 - - + -
1361C PHE* 1.3 79.9 - - - +
1363C TYR* 1.3 63.3 + - - +
1411C VAL* 4.1 15.5 - - + -
1442C PHE* 3.8 36.1 - - + -
1469C PHE* 4.2 15.5 - - + -
1471C THR* 3.4 28.3 - - + -
1475C LEU* 3.6 9.7 - - + +
1481C TRP* 3.1 3.1 - - - -
1482C PHE 2.9 32.1 + - - -
1484C VAL* 3.6 17.7 - - + -
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Residues in contact with TYR1363 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1198C ASP* 4.2 12.7 + - - +
1342C TYR* 3.3 8.9 - - - +
1343C PHE* 2.9 36.8 + - + +
1345C VAL* 4.0 29.2 - - + -
1347C TYR* 3.0 24.4 + + - -
1361C PHE* 4.0 17.7 - - + -
1362C ILE* 1.3 73.5 - - - +
1364C ARG* 1.3 61.7 + - - +
1365C GLY 3.6 0.9 + - - -
1374C PHE* 3.5 36.1 - + + -
1378C LEU* 4.3 7.1 - - + +
1480C ARG* 3.3 11.7 - - + -
1481C TRP* 3.3 56.7 + + + -
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Residues in contact with ARG1364 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1238C THR* 4.7 6.9 + - - -
1239C GLU* 4.4 16.8 + - - -
1291C GLY 5.4 2.0 + - - -
1293C MET* 4.2 18.0 - - - -
1340C PRO* 4.2 11.6 - - + +
1342C TYR* 3.4 37.9 + - + -
1363C TYR* 1.3 70.6 - - - +
1365C GLY* 1.3 63.5 + - - +
1437C ASN* 3.2 27.3 + - - -
1475C LEU* 4.0 10.4 - - + +
1476C PRO* 3.7 39.2 - - - +
1480C ARG* 2.6 54.1 + - - +
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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