Contacts of the strand formed by residues 1442 - 1450 (chain X) in PDB entry 2IWL
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 TYR1442 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1432X TYR* 3.5 35.6 - + + -
1433X HIS* 3.4 12.1 - - - -
1434X LYS* 3.9 39.1 + - + +
1440X LYS* 5.3 11.7 - - + -
1441X HIS* 1.3 86.1 + - - +
1443X ILE* 1.3 59.4 + - - +
1444X TYR* 4.3 26.6 - - + +
1462X THR* 4.5 8.5 - - - -
1463X PHE* 4.9 1.0 + - - +
1498X ASP* 2.9 42.3 + - + -
1500X ALA 6.1 0.9 - - - -
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Residues in contact with ILE1443 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1432X TYR* 3.3 2.8 - - - +
1433X HIS* 2.7 65.9 + - + +
1435X LYS* 4.0 35.7 - - + +
1441X HIS* 4.7 1.6 - - + -
1442X TYR* 1.3 76.0 - - - +
1444X TYR* 1.3 66.2 + - - +
1460X PHE* 3.9 31.4 - - + -
1461X ARG 3.6 21.8 - - - +
1462X THR* 3.9 19.3 - - + +
1536X ARG* 4.0 15.5 - - + +
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Residues in contact with TYR1444 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1429X VAL* 4.0 22.7 - - + -
1431X THR 3.9 0.9 - - - -
1432X TYR* 3.7 26.5 - + + -
1442X TYR* 4.3 21.0 - - + +
1443X ILE* 1.3 73.8 - - - +
1445X VAL* 1.3 63.4 + - - +
1446X VAL* 3.6 3.4 + - + +
1459X VAL 3.5 1.2 - - - +
1460X PHE* 3.4 5.5 - - - -
1461X ARG 2.9 46.3 + - - +
1462X THR 4.2 0.2 - - - -
1463X PHE* 4.0 22.9 - - + -
1466X PHE* 4.0 12.8 - + + -
1500X ALA 4.2 5.9 + - - -
1501X ALA* 5.2 1.7 - - - -
1503X ARG* 3.1 32.5 + - + +
1504X LYS* 3.9 20.4 - - + -
1507X LEU* 3.6 22.9 - - + -
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Residues in contact with VAL1445 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1429X VAL* 3.6 2.6 - - - -
1430X PHE* 2.7 41.4 + - + +
1431X THR* 3.0 34.2 + - + +
1433X HIS* 4.2 18.6 - - + -
1444X TYR* 1.3 71.5 - - - +
1446X VAL* 1.3 56.5 + - - +
1458X PHE* 3.7 30.7 - - + -
1459X VAL 3.5 3.1 - - - +
1460X PHE* 3.6 33.2 - - + -
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Residues in contact with VAL1446 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1427X VAL* 4.6 0.7 - - + -
1428X SER 3.5 11.2 - - - +
1429X VAL* 4.5 2.9 - - + +
1444X TYR* 3.9 13.0 - - + +
1445X VAL* 1.3 75.5 - - - +
1447X ARG* 1.3 64.1 + - - +
1448X ILE* 3.8 19.1 + - + +
1457X SER 3.6 0.3 - - - +
1458X PHE* 3.1 9.3 - - - -
1459X VAL* 2.7 48.5 + - + +
1461X ARG* 4.4 5.8 - - + -
1466X PHE* 3.6 31.4 - - + -
1511X LEU* 4.0 18.2 - - + -
1530X PHE* 5.1 1.8 - - + -
1531X PHE* 4.2 9.6 - - + -
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Residues in contact with ARG1447 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1426X GLU* 3.0 36.6 + - - +
1427X VAL* 3.1 9.2 - - - +
1428X SER* 2.8 42.6 + - - +
1430X PHE* 3.9 13.4 - - + -
1445X VAL 3.9 0.6 + - - -
1446X VAL* 1.3 72.3 - - - +
1448X ILE* 1.3 60.6 + - - +
1449X LEU* 4.3 12.3 - - - +
1454X ILE 5.4 1.2 + - - -
1456X PRO* 3.6 37.6 - - + +
1457X SER 3.6 3.1 - - - -
1458X PHE* 3.5 26.1 - - + -
2541X SO4 3.9 26.0 + - - -
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Residues in contact with ILE1448 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1424X ILE* 4.2 17.3 - - + -
1426X GLU 3.5 5.8 - - - +
1427X VAL* 3.7 15.9 - - + -
1446X VAL* 4.2 6.7 - - + +
1447X ARG* 1.3 76.5 - - - +
1449X LEU* 1.3 67.0 + - - +
1450X ARG* 3.8 28.6 + - + +
1453X GLN* 4.7 1.9 - - - +
1456X PRO* 3.3 3.9 - - - +
1457X SER* 2.8 51.0 + - - +
1459X VAL* 3.9 28.9 - - + -
1531X PHE* 3.9 34.3 - - + +
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Residues in contact with LEU1449 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1424X ILE* 3.9 2.4 - - - +
1425X LYS* 2.9 40.3 + - - +
1426X GLU* 2.9 52.9 + - + +
1447X ARG* 4.5 11.6 - - - +
1448X ILE* 1.3 74.5 - - - +
1450X ARG* 1.3 64.3 + - - +
1453X GLN* 3.6 22.2 - - + +
1454X ILE* 3.6 28.5 - - + +
1455X GLU 3.8 16.2 - - - +
1456X PRO* 3.8 5.8 - - + -
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Residues in contact with ARG1450 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1418X PHE* 3.9 14.8 - - - -
1421X ASP* 3.6 37.8 + - - +
1422X GLY* 2.8 39.1 + - - +
1423X ARG 3.2 10.3 - - - +
1424X ILE* 4.2 3.6 - - - +
1425X LYS* 4.2 6.6 - - - +
1448X ILE* 3.8 22.0 - - + +
1449X LEU* 1.3 79.7 - - - +
1451X GLU* 1.3 69.6 + - - +
1452X GLY 3.5 0.2 + - - -
1453X GLN* 3.2 56.4 + - - +
1457X SER* 5.3 4.1 + - - +
1528X CYS* 5.2 1.0 + - - -
1531X PHE* 3.6 33.5 + - - +
1532X HIS* 4.7 1.4 - - - +
1533X PRO* 4.7 5.5 - - - +
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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