Contacts of the strand formed by residues 1541 - 1550 (chain F) in PDB entry 1IV4
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 HIS1541 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1334E SER 4.1 5.8 + - - -
1335E GLU* 2.8 42.0 - - + +
1337E LEU* 3.7 30.4 + - + +
1409F SER* 4.8 3.0 + - - -
1410F HIS 3.3 8.1 + - - +
1411F ARG* 3.4 42.2 + - - -
1412F LEU* 3.5 12.9 - - - +
1499F THR 3.9 6.4 - - - +
1500F LEU* 4.0 6.8 - - - +
1501F ASP 5.0 0.7 + - - -
1538F ALA* 3.3 24.8 + - + +
1539F PRO 3.5 0.9 - - - +
1540F SER* 1.3 97.1 - - - +
1542F VAL* 1.3 65.6 + - - +
1543F GLN* 4.5 7.5 - - + +
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Residues in contact with VAL1542 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1409F SER* 3.2 6.6 - - - -
1410F HIS* 2.9 43.3 + - + +
1412F LEU* 3.8 20.1 - - + +
1418F LEU* 5.1 6.7 - - + -
1420F LEU* 4.2 24.9 - - + -
1431F ALA* 5.4 0.4 - - + -
1437F GLY 4.7 5.2 - - - +
1439F ALA* 4.2 12.5 - - + +
1498F LEU* 5.7 1.6 - - + -
1499F THR 3.5 8.7 - - - +
1500F LEU* 4.1 23.3 - - + -
1541F HIS* 1.3 74.9 - - - +
1543F GLN* 1.3 68.9 + - - +
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Residues in contact with GLN1543 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1337E LEU* 3.9 20.0 - - + +
1408F ASP 3.6 6.5 - - - +
1409F SER* 4.1 12.2 - - - -
1439F ALA* 4.6 2.2 - - - -
1497F VAL 4.5 0.4 - - - -
1498F LEU* 3.4 5.2 - - - +
1499F THR* 2.8 58.5 + - - +
1534F SER* 4.5 1.0 - - - -
1538F ALA* 3.4 21.5 - - - +
1541F HIS* 4.5 8.4 - - + +
1542F VAL* 1.3 81.7 - - - +
1544F ALA* 1.3 62.0 + - - +
1545F ARG* 3.1 39.5 - - - +
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Residues in contact with ALA1544 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1407F GLU* 3.3 0.5 - - - +
1408F ASP 2.9 31.5 + - - +
1439F ALA* 3.3 35.4 - - + +
1440F ALA* 4.0 1.8 - - - +
1443F ALA* 3.8 8.3 - - + -
1496F LEU* 5.1 1.8 - - + -
1497F VAL 3.3 5.2 - - - -
1498F LEU* 3.6 18.2 - - + -
1543F GLN* 1.3 76.5 - - - +
1545F ARG* 1.3 71.2 + - - +
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Residues in contact with ARG1545 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005D TYR* 3.8 14.0 - - + -
1007D GLU* 3.1 45.1 + - - +
1145D ARG* 3.6 27.9 - - - +
1343E GLN* 5.7 0.2 - - - +
1345E ARG* 3.6 17.9 - - - +
1405F TYR* 3.3 22.9 - - - +
1406F GLY 3.4 5.6 - - - +
1407F GLU* 2.9 28.6 + - + +
1443F ALA* 4.7 0.2 - - - -
1496F LEU* 3.1 3.5 - - - +
1497F VAL 2.9 31.9 + - - +
1499F THR* 4.6 5.9 + - - -
1543F GLN* 3.1 37.1 - - - +
1544F ALA* 1.3 80.9 - - - +
1546F ALA* 1.3 61.1 + - - +
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Residues in contact with ALA1546 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005D TYR* 5.2 0.2 - - - -
1405F TYR* 3.3 9.3 - - - -
1406F GLY 2.8 31.9 + - - +
1443F ALA* 4.1 24.0 - - + +
1444F LEU* 3.9 22.2 - - + -
1447F ALA* 4.0 3.7 - - + +
1495F SER 3.4 5.2 - - - +
1496F LEU* 3.6 16.4 - - + -
1545F ARG* 1.3 74.3 - - - +
1547F VAL* 1.3 63.6 + - - +
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Residues in contact with VAL1547 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003D ILE* 3.3 37.6 - - + +
1005D TYR* 4.0 29.4 - - + -
1147D VAL* 4.8 6.3 - - + -
1347E VAL* 4.9 3.6 - - + -
1403F ILE* 3.7 18.2 - - + -
1404F GLY 3.3 4.7 - - - +
1405F TYR* 3.7 20.9 - - + -
1493F GLN 4.2 0.2 - - - +
1494F ALA* 3.4 2.6 - - - +
1495F SER* 2.8 39.7 + - - +
1546F ALA* 1.3 76.4 - - - +
1548F VAL* 1.3 70.6 + - - +
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Residues in contact with VAL1548 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1003D ILE* 5.1 0.4 - - - -
1403F ILE* 3.2 11.6 - - - +
1404F GLY 2.8 37.6 + - - +
1444F LEU* 4.3 13.2 - - + +
1447F ALA* 3.6 39.3 - - + +
1448F LEU* 4.0 15.9 - - + +
1491F LEU* 4.2 9.4 - - + -
1493F GLN 3.4 10.8 - - - +
1494F ALA* 4.1 13.7 - - + -
1520F MET* 5.6 1.6 - - + -
1547F VAL* 1.3 82.2 - - - +
1549F LEU* 1.3 60.2 + - - +
1550F LEU* 3.9 15.5 - - + -
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Residues in contact with LEU1549 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1002D ARG* 4.3 10.5 - - - +
1003D ILE* 3.9 28.3 - - + +
1149D LEU* 6.1 5.8 - - + -
1349E LEU* 6.1 5.6 - - + -
1402F ARG 3.4 18.6 - - - +
1403F ILE* 5.2 8.7 - - + -
1491F LEU* 3.5 4.0 - - - +
1492F LEU* 2.8 49.5 + - + +
1493F GLN* 3.0 33.8 + - + +
1548F VAL* 1.3 74.1 - - - +
1550F LEU* 1.3 67.2 + - - +
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Residues in contact with LEU1550 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1402F ARG* 2.9 46.6 + - + +
1448F LEU* 4.2 12.1 - - + -
1451F ALA* 3.6 30.3 - - + -
1452F TYR* 4.6 4.5 - - + -
1484F VAL* 4.2 9.2 - - + -
1489F ALA* 3.9 22.2 - - + -
1490F LYS 3.3 7.9 - - - +
1491F LEU* 3.8 28.0 - - + +
1492F LEU* 4.1 1.3 - - - +
1548F VAL* 3.9 15.5 - - + -
1549F LEU* 1.3 86.3 - - - +
1551F ASP* 1.3 71.3 + - - +
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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