Contacts of the strand formed by residues 221 - 224 (chain 2) in PDB entry 1AFB
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 VAL 221 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1122 PHE* 4.3 7.0 - - + -
1132 VAL 3.4 11.4 - - - +
1142 THR* 3.9 9.9 - - - -
1242 VAL* 4.5 2.2 - - - +
1282 CYS* 3.8 1.8 - - - -
1352 VAL* 3.8 9.2 - - - +
1362 ALA* 3.0 41.1 + - + +
1472 ILE* 4.3 8.5 - - + -
1502 VAL* 4.2 14.6 - - + -
1512 ALA* 3.8 17.5 - - + -
1552 ALA* 3.7 27.1 - - + -
1562 PHE 4.8 3.2 + - - +
2192 THR* 3.6 4.8 + - + -
2202 ALA* 1.3 79.2 - - - +
2222 CYS* 1.3 68.9 + - - +
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Residues in contact with CYS 222 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011 PHE* 3.9 25.6 - - + -
1112 PHE 3.8 0.3 - - - +
1122 PHE* 3.3 4.0 - - - -
1132 VAL* 2.9 35.2 + - - +
1272 LEU* 4.6 1.1 - - - -
1282 CYS* 2.0 55.2 - - + -
1312 LEU* 4.1 5.4 - - - -
1342 THR 3.3 6.7 - - - +
1362 ALA 4.4 0.4 - - - -
2202 ALA* 5.3 0.4 - - - -
2212 VAL* 1.3 78.2 - - - +
2232 GLU* 1.3 61.8 + - - +
2242 PHE* 3.9 21.3 - - + -
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Residues in contact with GLU 223 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1102 LYS* 3.2 39.7 + - + +
1112 PHE 3.1 4.9 - - - +
1122 PHE* 3.5 22.1 - - + -
1332 GLY* 3.5 7.3 - - - -
1342 THR* 2.8 47.7 + - - +
1352 VAL 4.6 0.2 - - - -
1362 ALA* 4.1 3.8 - - - +
1372 ILE* 2.7 36.5 + - - +
1392 ARG* 5.4 2.4 + - - -
2222 CYS* 1.3 74.3 - - - +
2242 PHE* 1.3 66.5 + - - +
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Residues in contact with PHE 224 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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981 LEU* 3.8 26.9 - - + -
1102 LYS* 3.4 8.8 - - - +
1112 PHE* 2.8 61.6 + + + +
1132 VAL* 3.3 26.7 - - + -
1312 LEU* 3.4 35.0 - - + -
1322 ARG 4.1 5.2 - - - -
1332 GLY* 3.7 16.2 - - - -
2222 CYS* 3.9 20.4 - - + -
2232 GLU* 1.3 77.9 - - - +
2252 PRO* 1.3 74.5 - - + +
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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