Contacts of the helix formed by residues 258 - 263 (chain 2) in PDB entry 1MVW
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 PRO 258 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1852 LEU* 5.1 1.1 - - + -
2172 CYS* 4.1 3.1 - - + -
2182 TYR 3.2 22.9 - - - +
2192 VAL* 3.3 26.9 - - + -
2232 PHE* 4.1 2.7 - - - -
2542 ARG 3.7 7.4 - - - +
2552 PHE 3.6 3.1 - - - +
2572 CYS* 1.3 88.4 - - + +
2592 GLU* 1.4 59.3 + - - +
2602 THR 2.9 6.1 - - - -
2612 LEU* 2.9 25.2 + - + +
2622 PHE* 3.8 7.3 - - - -
3062 TYR* 3.6 43.5 - - + -
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Residues in contact with GLU 259 (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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2232 PHE* 3.1 59.7 - - + +
2242 GLU* 4.5 0.9 + - - -
2272 MET* 3.9 23.2 - - - +
2552 PHE* 3.1 25.7 + - - +
2562 ARG* 3.9 1.8 - - - +
2572 CYS 3.3 0.2 - - - -
2582 PRO* 1.4 73.5 - - - +
2602 THR* 1.4 60.4 + - - +
2622 PHE* 3.2 1.8 + - - -
2632 GLN* 2.7 58.5 + - - +
2662 PHE* 3.6 27.6 - - + -
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Residues in contact with THR 260 (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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1802 LEU* 4.4 3.3 - - + +
1852 LEU* 4.3 15.9 - - + -
1882 TYR* 3.2 25.4 - - + -
2562 ARG 3.4 1.5 + - - -
2572 CYS 2.6 21.3 + - - -
2582 PRO 2.9 0.8 - - - -
2592 GLU* 1.4 77.2 - - - +
2612 LEU* 1.3 58.6 + - - +
2632 GLN 2.7 32.4 - - - +
2642 PRO* 3.4 5.2 - - - +
2662 PHE* 3.9 6.0 - - + -
2672 ILE* 3.6 47.1 - - + -
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Residues in contact with LEU 261 (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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1552 SER* 4.8 4.3 - - - +
1782 LEU* 5.1 0.5 - - - +
1802 LEU* 3.5 30.7 - - + +
1852 LEU* 4.0 15.9 - - + -
2192 VAL* 5.6 0.7 - - + -
2582 PRO* 2.9 14.2 + - + +
2602 THR* 1.3 78.4 - - - +
2622 PHE* 1.3 63.7 + - + +
2642 PRO* 4.7 1.6 - - - +
2732 GLY* 3.8 3.3 - - - -
2742 ILE* 3.2 53.1 + - + +
3032 THR* 4.1 17.0 - - + +
3062 TYR* 4.0 31.9 - - + -
3092 ILE* 4.3 13.5 - - + -
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Residues in contact with PHE 262 (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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2192 VAL* 3.5 27.8 - - + -
2232 PHE* 3.9 4.3 - + - -
2582 PRO 3.8 14.1 - - - -
2592 GLU* 3.2 2.4 + - - -
2612 LEU* 1.3 78.4 - - + +
2632 GLN* 1.3 75.2 + - - +
2642 PRO* 3.6 8.1 - - - +
2732 GLY* 4.0 4.3 + - - -
2742 ILE* 3.6 26.2 - - + -
2752 HIS* 3.4 40.1 - - + +
3092 ILE* 4.6 11.0 - - + -
3122 ARG* 3.3 51.4 - - + +
3132 MET* 4.2 17.5 - - + -
3162 GLU* 4.0 2.7 - - + -
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Residues in contact with GLN 263 (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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2592 GLU* 2.7 64.6 + - - +
2602 THR* 2.7 23.6 - - - +
2622 PHE* 1.3 93.7 - - - +
2642 PRO* 1.3 59.4 - - - +
2652 SER* 3.1 19.8 + - - +
2662 PHE* 3.5 26.3 + - + +
3122 ARG* 3.4 10.1 + - - +
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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