Contacts of the strand formed by residues 304 - 309 (chain P) in PDB entry 1HH2
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 ALA 304 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298P LEU* 2.9 33.5 + - + -
299P ASP* 3.2 22.5 + - + -
302P ASN* 4.4 4.3 - - + +
303P LYS* 1.3 78.2 - - - +
305P ALA* 1.3 63.0 + - - +
334P TRP* 3.5 6.6 - - - -
335P LYS* 3.6 21.5 - - + -
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Residues in contact with ALA 305 (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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283P ILE* 4.2 8.7 - - + -
295P VAL* 4.0 20.2 - - + -
296P GLU 3.3 13.5 - - - +
297P ILE* 4.4 0.4 - - - -
298P LEU* 3.7 11.3 - - - +
304P ALA* 1.3 76.0 - - - +
306P ARG* 1.3 60.5 + - - +
307P VAL* 4.1 3.8 - - + -
334P TRP* 4.0 15.5 - - + -
335P LYS 2.9 11.2 + - - +
336P ILE* 3.5 4.5 - - + -
337P ASP* 2.9 24.8 + - - +
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Residues in contact with ARG 306 (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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294P GLU 4.0 0.9 - - - +
295P VAL* 3.7 0.3 - - - -
296P GLU* 2.5 78.9 + - - +
298P LEU* 3.4 26.5 - - + +
305P ALA* 1.3 73.8 - - - +
307P VAL* 1.3 62.8 + - - +
308P LEU* 4.1 20.4 + - + +
337P ASP* 3.4 24.5 - - - +
339P LYS* 4.5 19.5 - - + +
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Residues in contact with VAL 307 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283P ILE* 3.7 27.1 - - + -
287P LEU* 3.7 11.0 - - + -
292P VAL* 3.6 38.1 - - + -
294P GLU 3.7 2.7 - - - -
295P VAL* 4.4 8.3 - - + -
305P ALA* 4.8 1.8 - - + +
306P ARG* 1.3 78.4 - - - +
308P LEU* 1.3 64.7 + - - +
309P VAL* 3.9 8.9 + - + -
336P ILE* 3.8 23.3 - - + -
337P ASP 2.7 11.7 + - - +
338P ILE* 3.4 5.5 - - + +
339P LYS* 2.8 28.8 + - - +
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Residues in contact with LEU 308 (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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292P VAL* 3.6 3.3 - - - +
293P ILE* 2.7 31.8 + - + -
294P GLU* 3.0 46.8 + - + +
296P GLU* 3.8 21.8 - - - +
306P ARG* 4.1 21.1 - - - +
307P VAL* 1.3 75.8 - - - +
309P VAL* 1.3 58.2 + - - +
339P LYS* 3.2 28.7 - - + +
340P PRO 4.5 4.5 - - - +
341P ILE* 3.1 26.0 - - + -
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Residues in contact with VAL 309 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287P LEU* 5.8 0.2 - - + -
290P ALA* 5.6 0.9 - - + -
291P THR 3.8 11.7 - - - +
292P VAL* 4.2 7.2 - - + -
307P VAL* 4.1 17.0 - - + -
308P LEU* 1.3 79.3 - - - +
310P PRO* 1.3 80.9 - - + +
313P GLN* 4.0 6.5 - - + +
314P LEU* 3.8 18.2 - - - -
317P ALA* 4.2 16.8 - - + -
338P ILE* 3.8 18.6 - - + -
339P LYS 2.8 20.9 + - - +
340P PRO* 3.0 7.7 - - + +
341P ILE* 2.8 30.9 + - - +
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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