Contacts of the strand formed by residues 231 - 238 (chain A) in PDB entry 3IND
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 SER 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A ARG* 5.8 5.6 - - - -
70A GLY 3.6 6.2 + - - -
71A LYS* 3.1 25.8 + - - +
218A GLY 3.9 0.2 - - - +
219A ALA* 3.8 17.3 - - - +
229A LEU 3.6 0.4 + - - -
230A ALA* 1.3 74.0 - - - +
232A VAL* 1.3 63.3 + - - +
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Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ARG* 3.5 12.6 - - - -
70A GLY* 2.8 53.4 + - - +
71A LYS 4.1 5.4 - - - +
72A SER* 4.1 24.9 - - - -
75A GLY 4.5 1.8 - - - +
76A TYR* 3.5 26.2 - - + +
218A GLY* 3.1 35.4 - - - +
219A ALA* 3.7 4.3 - - + +
231A SER* 1.3 77.9 - - - +
233A GLY* 1.3 59.1 + - - +
401A GLU* 4.9 2.0 - - - +
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Residues in contact with GLY 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ASP* 4.3 3.1 - - - -
68A LEU 3.5 10.5 - - - -
69A ARG* 3.6 12.8 - - - -
76A TYR* 3.3 10.7 - - - -
217A CYS* 3.0 30.8 + - - +
218A GLY 3.3 6.1 + - - -
232A VAL* 1.3 74.7 - - - +
234A GLY* 1.3 58.2 + - - -
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Residues in contact with GLY 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ASP* 3.0 19.2 + - - -
68A LEU* 3.0 35.9 + - - +
76A TYR* 4.7 0.7 - - - -
215A GLN 3.0 14.8 - - - -
216A LEU* 4.5 1.6 - - - -
217A CYS* 4.3 8.3 - - - -
233A GLY* 1.3 74.1 - - - -
235A SER* 1.3 63.5 + - - -
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Residues in contact with SER 235 (chain A).
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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64A MET 3.9 6.5 - - - -
65A VAL* 3.5 9.1 - - - +
66A ASP* 2.7 26.5 + - - -
67A ASN* 3.5 5.4 - - - -
68A LEU* 3.7 6.1 - - - +
213A SER 3.7 1.0 - - - +
214A LEU* 3.4 3.3 - - - -
215A GLN* 2.8 49.7 + - - +
234A GLY* 1.3 74.1 - - - -
236A MET* 1.3 61.1 + - - +
237A ILE* 3.8 16.6 - - - +
245A LEU* 4.1 11.9 - - - +
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Residues in contact with MET 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A MET* 3.8 6.2 - - - +
67A ASN* 2.8 28.0 + - - +
68A LEU* 3.5 13.4 - - + +
78A VAL* 3.9 37.0 - - + -
93A VAL* 3.9 25.8 - - + -
149A ILE* 4.4 5.4 - - + -
181A LEU* 4.6 6.7 - - + -
183A LEU* 4.1 14.1 - - - -
212A PHE* 4.8 6.3 - - + -
213A SER 3.4 5.6 - - - +
214A LEU* 3.6 15.5 - - + -
235A SER* 1.3 71.9 - - - +
237A ILE* 1.3 64.1 + - - +
238A ILE* 3.5 40.1 + - + +
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Residues in contact with ILE 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A PHE* 3.5 46.0 - - + +
64A MET* 3.9 23.3 - - + -
65A VAL* 4.4 1.1 - - - +
212A PHE* 3.3 3.5 - - - +
213A SER* 2.8 46.8 + - - +
235A SER* 4.0 12.3 - - - +
236A MET* 1.3 74.3 - - - +
238A ILE* 1.3 60.4 + - - +
240A GLY 3.4 17.7 - - - +
242A ASP* 4.0 7.2 - - + +
245A LEU* 3.5 32.1 - - + -
404A TYR* 3.6 9.9 - - + +
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Residues in contact with ILE 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A PHE* 4.1 5.2 - - - -
64A MET* 3.5 24.0 - - - +
67A ASN* 5.5 0.2 - - - +
149A ILE* 3.5 32.3 - - + -
152A GLY* 4.9 3.8 - - - -
153A PRO* 3.8 25.2 - - + +
181A LEU* 6.1 0.4 - - + -
198A PHE* 5.9 0.7 - - + -
199A PHE* 3.7 13.9 - - + -
202A LEU* 3.7 28.7 - - + -
208A VAL* 3.9 10.7 - - + +
212A PHE* 4.2 7.6 - - + -
236A MET* 3.5 35.2 - - + +
237A ILE* 1.3 73.3 - - - +
239A GLY* 1.3 64.0 + - - +
240A GLY 3.5 0.4 - - - -
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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