Contacts of the strand formed by residues 89 - 94 (chain P) in PDB entry 1HI0
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 HIS 89 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45P SER 5.4 0.3 - - - +
51P LEU* 5.1 0.5 - - - +
54P LYS* 3.6 13.2 + - - +
86P GLY 2.7 28.0 - - - -
87P MET 2.7 10.3 + - - +
88P ARG* 1.3 76.0 - - - +
90P MET* 1.3 68.6 + - - +
91P ASN* 3.1 17.5 + - - +
206P GLN 5.8 0.2 - - - -
207P SER 3.5 21.8 - - - +
208P THR* 3.9 0.4 - - - -
209P ASP* 3.2 38.8 + - + -
211P ILE* 3.5 22.4 - - + +
247P LYS* 5.0 7.9 - - + -
264P PHE* 4.4 1.2 - - - -
265P PHE* 3.2 13.9 + - + +
266P CYS 3.4 22.8 + - - -
267P GLU* 4.3 12.7 - - + -
268P ARG 5.4 0.9 - - - -
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Residues in contact with MET 90 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45P SER* 4.6 1.8 - - - -
46P VAL* 4.0 18.4 - - + -
51P LEU* 3.2 44.6 - - + -
89P HIS* 1.3 73.1 - - - +
91P ASN* 1.3 64.7 + - - +
92P GLY 3.1 0.2 + - - -
93P PHE* 3.0 28.9 + - + +
249P ALA* 4.1 12.8 - - + -
252P LEU* 3.8 29.4 - - + -
258P ILE* 5.2 0.7 - - - -
259P ASP 5.1 1.3 - - - +
260P VAL* 4.6 13.9 - - - -
261P PRO* 5.0 0.2 - - - -
264P PHE* 3.4 28.9 - - + -
265P PHE 2.8 19.9 + - - +
266P CYS* 5.1 0.2 - - - -
267P GLU* 4.7 1.6 - - - -
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Residues in contact with ASN 91 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36P ALA* 3.7 3.3 - - - -
37P ILE* 3.4 31.3 + - + +
39P THR* 4.6 1.4 + - - -
45P SER* 2.8 38.7 + - - -
50P PHE* 5.0 0.2 - - - -
54P LYS* 3.1 25.2 - - - +
89P HIS* 3.1 10.1 + - - +
90P MET* 1.3 68.9 - - - +
92P GLY* 1.3 58.2 + - - +
93P PHE* 4.3 0.5 - - - -
207P SER* 3.8 10.0 - - - +
267P GLU* 3.2 22.0 - - - +
526P PHE 3.5 11.9 + - - -
527P SER* 3.6 22.4 + - - +
528P PRO* 4.5 3.4 - - - +
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Residues in contact with GLY 92 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34P GLU* 3.6 2.9 - - - +
35P GLY 3.0 38.3 + - - +
37P ILE* 3.5 12.8 - - - +
91P ASN* 1.3 73.7 - - - +
93P PHE* 1.3 61.2 + - - +
94P PRO* 3.6 9.1 - - - +
267P GLU* 2.9 15.3 + - - -
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Residues in contact with PHE 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34P GLU* 3.4 18.4 - - + +
35P GLY* 3.5 14.6 - - - -
36P ALA* 3.3 33.7 - - - -
46P VAL* 3.8 16.6 - - + -
90P MET* 3.0 21.4 + - + +
91P ASN 4.3 0.4 - - - -
92P GLY* 1.3 79.5 - - - +
94P PRO* 1.3 57.4 - - - +
252P LEU* 3.2 41.7 - - + -
256P TYR* 3.6 18.4 - + - -
258P ILE* 3.7 20.2 - - + -
266P CYS* 3.3 15.2 - - - +
267P GLU* 2.7 33.5 + - - +
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Residues in contact with PRO 94 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32P PHE* 3.5 26.9 - - + -
33P LYS 4.8 0.4 - - - +
34P GLU* 3.4 18.8 - - + +
92P GLY 3.6 9.2 - - - +
93P PHE* 1.3 83.5 - - - +
95P MET* 1.3 69.1 + - - +
96P ILE* 3.8 0.2 - - - +
251P ARG* 3.1 22.2 + - - -
266P CYS* 3.4 5.8 - - - +
267P GLU* 3.4 10.5 - - + +
269P ARG* 3.5 45.5 - - + +
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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