Contacts of the strand formed by residues 1447 - 1457 (chain B) in PDB entry 1W21
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 THR1447 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1122B VAL* 3.2 19.9 - - - +
1123B THR 4.0 2.1 - - - +
1124B ARG* 3.9 25.9 - - + +
1142B GLN* 5.3 0.3 - - - +
1154B THR* 3.1 10.5 + - - +
1155B ILE* 3.3 34.1 - - + +
1435B ILE* 4.1 7.9 - - + -
1436B ARG 3.5 9.4 - - - +
1438B ARG* 2.9 38.3 + - - +
1446B TRP* 1.3 72.0 - - - +
1448B SER* 1.3 63.7 + - - +
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Residues in contact with SER1448 (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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1112B ILE* 3.8 9.5 - - - +
1121B LEU 4.3 2.6 + - - -
1122B VAL* 3.7 13.5 - - - -
1123B THR* 3.2 28.5 + - - -
1124B ARG* 4.5 2.0 - - - +
1146B LEU* 3.9 22.9 - - - +
1435B ILE* 3.4 7.4 - - - +
1436B ARG 2.9 28.3 + - - +
1446B TRP* 3.6 3.5 - - - -
1447B THR* 1.3 77.1 - - - +
1449B ASN* 1.3 75.5 + - - +
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Residues in contact with ASN1449 (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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1111B ALA* 3.9 8.7 - - - +
1112B ILE* 3.5 17.2 - - - +
1123B THR* 2.7 54.1 + - - -
1124B ARG* 3.1 10.0 - - + +
1126B PRO* 3.6 18.1 - - - +
1433B GLU* 3.6 26.0 - - + +
1434B LEU 3.1 15.9 - - - +
1435B ILE* 4.1 2.0 - - + -
1436B ARG 4.4 0.2 - - - +
1448B SER* 1.3 83.5 + - - +
1450B SER* 1.3 71.9 + - - +
1451B ILE* 3.9 4.9 - - - +
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Residues in contact with SER1450 (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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1108B LYS* 4.6 2.1 + - - -
1109B ASP* 3.4 13.7 - - - -
1110B ASN* 4.4 3.4 - - - -
1111B ALA* 3.7 18.8 - - - -
1112B ILE* 4.2 1.8 - - - +
1433B GLU* 3.9 1.0 - - - -
1434B LEU* 3.0 45.7 + - - +
1449B ASN* 1.3 79.6 - - - +
1451B ILE* 1.3 66.0 + - - +
1468B ASP* 2.6 29.0 + - - +
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Residues in contact with ILE1451 (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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1108B LYS* 3.3 9.0 - - - +
1109B ASP* 2.8 39.9 + - - +
1110B ASN 4.5 0.3 + - - -
1126B PRO* 3.7 30.3 - - + -
1127B TYR 4.9 1.3 - - - +
1128B LEU* 4.0 21.8 - - + -
1137B MET* 4.0 23.8 - - + -
1138B PHE 4.4 1.3 - - - +
1139B ALA* 5.4 0.2 - - + -
1167B TRP* 3.7 31.2 - - + -
1431B TYR* 4.1 9.6 - - + -
1432B VAL 3.9 5.2 - - - +
1434B LEU* 4.4 3.1 - - - -
1449B ASN* 3.9 3.4 - - - +
1450B SER* 1.3 82.7 + - - +
1452B VAL* 1.3 75.6 + - - +
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Residues in contact with VAL1452 (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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1105B ILE* 3.8 15.3 - - + -
1107B SER 3.5 11.0 - - - +
1108B LYS* 4.1 8.1 - - + +
1403B ILE* 4.6 8.5 - - + -
1404B VAL* 4.9 0.4 - - + -
1431B TYR* 3.1 4.3 - - - +
1432B VAL* 2.9 56.9 + - + +
1434B LEU* 4.0 15.3 - - + -
1451B ILE* 1.3 76.4 - - - +
1453B ALA* 1.3 63.5 + - - +
1454B LEU* 4.2 6.2 - - + +
1466B TRP* 3.5 37.9 - - + +
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Residues in contact with ALA1453 (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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1105B ILE* 3.5 2.4 - - - +
1106B LEU* 2.8 31.6 + - + -
1107B SER* 2.7 29.8 + - - +
1128B LEU* 4.2 24.9 - - + -
1137B MET* 5.5 0.2 - - + -
1416B PHE* 4.2 12.6 - - + -
1430B PHE 3.2 11.9 - - - +
1451B ILE* 5.0 1.1 - - + -
1452B VAL* 1.3 76.6 - - - +
1454B LEU* 1.4 64.3 + - - +
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Residues in contact with LEU1454 (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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1103B TRP* 4.1 21.8 - - + +
1104B HIS 3.1 25.6 - - - +
1105B ILE* 4.1 5.4 - - + +
1106B LEU* 3.9 2.2 - - - +
1401B GLN* 4.3 7.9 - - - +
1403B ILE* 3.6 31.2 - - + -
1429B CYS* 3.1 4.5 - - - +
1430B PHE* 2.8 57.6 + - + +
1452B VAL* 4.2 13.5 - - + +
1453B ALA* 1.4 84.9 - - - +
1455B CYS* 1.3 62.9 + - - +
1466B TRP* 4.1 22.7 - - + +
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Residues in contact with CYS1455 (chain B).
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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1103B TRP* 3.3 8.0 - - - -
1104B HIS* 2.8 51.5 + - - +
1106B LEU* 3.7 30.1 - - - -
1427B ASN* 3.9 7.2 - - - +
1428B PRO 3.3 5.4 - - - +
1429B CYS* 2.0 46.7 - - - +
1454B LEU* 1.3 74.1 - - - +
1456B GLY* 1.3 64.3 + - - +
3218D PRO* 5.3 3.6 - - + -
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Residues in contact with GLY1456 (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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1100B VAL* 3.8 11.7 - - - -
1102B SER 3.6 8.1 - - - -
1103B TRP* 3.4 11.7 - - - -
1104B HIS* 3.4 9.7 + - - -
1423B LYS* 5.6 0.3 + - - -
1427B ASN* 2.7 35.5 + - - +
1428B PRO 2.9 13.7 + - - -
1455B CYS* 1.3 75.7 - - - +
1457B SER* 1.3 57.8 + - - -
3221D GLU* 4.8 1.9 - - - +
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Residues in contact with SER1457 (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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1099B GLU 4.3 4.9 - - - -
1100B VAL* 3.7 0.3 - - - -
1101B ASN 2.8 24.3 + - - -
1102B SER* 2.9 18.4 + - - -
1104B HIS* 4.5 2.5 - - - -
1427B ASN* 5.4 0.2 - - - +
1456B GLY* 1.3 75.1 - - - -
1458B LYS* 1.3 57.6 + - - +
1459B LYS* 3.0 22.3 + - - +
1461B LEU* 3.6 24.0 - - - +
3221D GLU* 2.7 28.7 + - - -
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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