Contacts of the helix formed by residues 302 - 309 (chain P) in PDB entry 3H1J
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 LEU 302 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99P ILE* 4.2 19.3 - - + -
114P TRP* 2.8 41.4 + - + +
118P VAL* 4.1 18.8 - - + -
121P LEU* 3.6 30.1 - - + -
299P VAL* 3.1 19.2 + - + +
300P LEU 2.9 0.4 + - - -
301P ILE* 1.3 85.1 - - + +
303P PHE* 1.3 60.5 + - - +
304P LEU 3.3 0.5 + - - -
305P ILE* 3.5 21.4 + - + +
359P TYR* 5.5 0.7 - - - +
363P LEU* 6.1 1.6 - - + -
502P HEM 4.3 12.6 - - + -
3007P PEE 4.3 25.4 - - + -
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Residues in contact with PHE 303 (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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114P TRP* 4.8 0.4 - - - +
115P ASN* 3.4 37.0 - - + +
118P VAL* 3.5 39.7 - - + -
119P ILE* 3.9 21.1 - - + -
122P LEU* 4.6 3.4 - - + -
300P LEU* 2.9 44.7 + - + +
302P LEU* 1.3 78.3 - - - +
304P LEU* 1.3 61.3 + - + +
306P PRO* 3.2 15.3 - - - +
307P PHE* 3.4 17.8 - - + -
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Residues in contact with LEU 304 (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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300P LEU 5.4 0.2 - - - +
301P ILE* 2.8 23.8 + - + +
303P PHE* 1.3 79.4 - - + +
305P ILE* 1.3 67.1 + - - +
306P PRO* 3.1 4.3 - - - -
307P PHE* 2.6 35.0 + - + +
308P LEU* 3.3 20.0 + - + +
364P LEU* 4.1 22.4 - - + -
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Residues in contact with ILE 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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103P LEU* 3.6 25.8 - - + -
108P TYR* 3.6 31.3 - - + -
114P TRP* 4.2 11.0 - - + +
301P ILE* 3.5 6.7 + - + +
302P LEU* 3.5 30.3 - - + +
304P LEU* 1.3 75.4 - - - +
306P PRO* 1.3 63.3 - - + +
308P LEU* 2.9 33.3 + - + +
309P HIS* 3.5 4.5 + - - -
363P LEU* 3.8 36.8 - - + +
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Residues in contact with PRO 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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108P TYR* 3.7 34.5 - - + +
109P LEU* 4.5 5.2 - - + +
111P LYS* 3.9 32.7 + - + +
114P TRP* 3.8 17.9 - - + +
115P ASN* 5.2 3.6 - - - +
302P LEU 3.6 5.6 - - - +
303P PHE 3.2 12.8 - - - +
304P LEU 3.1 5.6 - - - -
305P ILE* 1.3 95.9 - - + +
307P PHE* 1.3 64.6 + - + +
308P LEU 3.2 0.9 + - - -
309P HIS* 3.7 15.4 + - - +
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Residues in contact with PHE 307 (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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111P LYS* 3.2 37.0 - - + -
115P ASN* 5.9 3.4 - - - -
303P PHE* 3.4 20.2 - - + -
304P LEU* 2.6 36.1 + - + +
306P PRO* 1.3 74.9 - - + +
308P LEU* 1.3 65.5 + - + +
309P HIS 3.4 2.8 - - - +
310P LYS* 4.6 10.7 + - - -
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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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301P ILE* 6.0 0.7 - - + -
304P LEU* 3.8 23.3 - - + +
305P ILE* 2.9 18.4 + - + +
307P PHE* 1.3 85.9 - - + +
309P HIS* 1.3 61.7 + - - +
310P LYS* 3.3 10.1 + - - +
363P LEU* 2.8 34.8 - - + +
364P LEU* 3.8 29.2 - - + +
367P PHE* 4.9 4.4 - - + +
368P PRO* 3.7 29.2 - - + +
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Residues in contact with HIS 309 (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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108P TYR* 2.6 46.0 + + + -
109P LEU* 4.1 27.0 - - + +
305P ILE 3.5 2.0 + - - -
306P PRO 3.8 10.7 - - - +
307P PHE 3.4 3.3 - - - +
308P LEU* 1.3 77.4 - - - +
310P LYS* 1.3 64.5 + - - +
311P SER* 3.3 27.2 + - - -
313P GLN 3.2 28.5 + - - -
314P ARG* 3.6 17.0 - - - -
319P ARG* 4.3 4.4 + - - -
38S TYR* 5.4 4.7 - + - -
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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