Contacts of the strand formed by residues 1217 - 1223 (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 ARG1217 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ASP 3.0 24.2 + - - -
132A PRO 2.9 21.0 + - - -
133A GLN 3.8 11.7 + - - +
134A GLY* 3.7 13.2 - - - +
418A ASP* 2.5 42.5 + - - +
420A TRP* 3.6 14.5 + - - +
421A ALA* 4.0 16.6 - - + +
422A ASN* 5.1 2.9 - - - +
1213B TRP* 3.3 4.6 - - - -
1214B TYR 2.8 37.7 + - - +
1215B GLY 4.6 6.6 + - - +
1216B GLY* 1.3 84.1 - - - +
1218B PRO* 1.3 71.7 - - + +
1219B ILE* 3.4 11.2 + - + +
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Residues in contact with PRO1218 (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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104A HIS* 3.7 30.1 - - + +
106A LEU* 3.7 20.4 - - + -
418A ASP* 5.4 4.0 - - - +
423A LYS* 4.6 15.0 + - - -
455A CYS* 5.4 3.1 - - + -
1211B VAL* 4.2 3.8 - - + -
1212B VAL 3.9 5.2 - - - +
1213B TRP* 3.6 29.6 - - + -
1216B GLY 4.5 0.2 - - - +
1217B ARG* 1.3 86.8 - - + +
1219B ILE* 1.3 67.0 + - - +
1220B THR 3.9 0.2 - - - -
1221B GLU* 5.5 1.6 - - - +
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Residues in contact with ILE1219 (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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422A ASN* 6.0 7.4 - - + +
423A LYS* 5.2 9.6 + - - +
1212B VAL 2.7 15.0 + - - +
1214B TYR* 3.5 33.4 - - + +
1217B ARG* 3.4 24.5 - - + +
1218B PRO* 1.3 78.0 - - - +
1220B THR* 1.3 61.3 + - - +
1221B GLU* 3.9 7.7 - - - +
1266B GLU 3.7 9.2 - - - +
1267B GLY* 3.4 28.9 - - - +
1268B LYS* 4.0 13.7 - - + -
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Residues in contact with THR1220 (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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459A LYS* 4.3 6.7 - - - +
1211B VAL* 3.3 5.0 - - - +
1212B VAL* 2.6 41.4 + - + +
1219B ILE* 1.3 84.5 + - - +
1221B GLU* 1.3 82.2 + - - +
1222B ILE* 4.3 4.0 - - + -
1267B GLY 2.6 27.3 + - - -
1268B LYS* 3.9 5.7 - - - +
1269B ILE* 4.0 29.8 - - + +
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Residues in contact with GLU1221 (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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104A HIS* 4.0 34.3 + - + +
423A LYS* 5.3 5.9 + - - -
456A GLY 4.8 1.5 - - - +
457A SER* 2.6 36.1 + - - +
458A LYS 4.3 1.6 + - - -
459A LYS* 3.0 35.6 + - + +
461A LEU* 3.8 20.0 - - + -
1210B ALA 3.2 8.7 - - - +
1211B VAL* 4.6 4.5 - - + -
1218B PRO* 5.4 1.6 - - - +
1219B ILE 3.9 5.5 + - - +
1220B THR* 1.3 89.5 + - - +
1222B ILE* 1.3 67.4 + - - +
1223B PRO* 4.3 1.3 - - - -
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Residues in contact with ILE1222 (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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459A LYS* 5.3 0.2 - - - +
461A LEU* 4.3 2.9 - - - +
1209B SER* 3.3 1.7 - - - -
1210B ALA* 2.8 45.8 + - + +
1212B VAL* 4.2 9.2 - - + -
1220B THR* 4.3 3.8 - - + -
1221B GLU* 1.3 79.1 - - - +
1223B PRO* 1.3 77.5 - - + +
1225B TRP* 4.1 22.4 - - + -
1230B LEU* 3.6 4.3 - - + +
1248B MET* 4.2 15.0 - - + -
1262B ILE* 4.2 7.6 - - + -
1264B PHE* 3.9 33.2 - - + -
1269B ILE* 4.1 22.2 - - + -
1272B ILE* 6.4 1.3 - - + -
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Residues in contact with PRO1223 (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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459A LYS* 4.6 17.3 - - + +
460A ARG 3.9 22.0 - - - +
461A LEU* 3.9 21.1 - - + -
462A GLY 5.3 1.6 - - - +
1208B ALA 4.1 4.5 - - - +
1209B SER* 4.3 0.9 - - - -
1221B GLU 4.1 3.6 - - - +
1222B ILE* 1.3 100.6 - - + +
1224B SER* 1.3 70.6 + - - +
1225B TRP* 3.5 8.0 + - - +
1230B LEU* 4.1 1.1 - - - +
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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