Contacts of the helix formed by residues 258 - 263 (chain 7) 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 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1857 LEU* 5.1 0.9 - - + -
2177 CYS* 4.1 2.9 - - + -
2187 TYR 3.2 21.8 - - - +
2197 VAL* 3.3 26.0 - - + -
2237 PHE* 4.1 2.5 - - - -
2547 ARG 3.7 8.3 - - - +
2557 PHE 3.6 3.8 - - - +
2577 CYS* 1.3 88.3 - - + +
2597 GLU* 1.4 59.7 + - - +
2607 THR 2.9 5.4 - - - -
2617 LEU* 2.9 24.7 + - + +
2627 PHE* 3.8 7.3 - - - -
3067 TYR* 3.6 44.2 - - + -
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Residues in contact with GLU 259 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2237 PHE* 3.1 59.2 - - + +
2247 GLU* 4.5 0.5 + - - -
2277 MET* 3.9 23.3 - - - +
2557 PHE* 3.1 25.0 + - - +
2567 ARG* 3.9 2.3 - - - +
2577 CYS 3.3 0.2 - - - -
2587 PRO* 1.4 73.1 - - - +
2607 THR* 1.4 59.6 + - - +
2627 PHE* 3.2 2.2 + - - -
2637 GLN* 2.7 59.0 + - - +
2667 PHE* 3.6 27.1 - - + -
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Residues in contact with THR 260 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1807 LEU* 4.4 3.2 - - + +
1857 LEU* 4.3 15.9 - - + -
1887 TYR* 3.2 25.3 - - + -
2567 ARG 3.4 1.7 + - - -
2577 CYS 2.6 20.8 + - - -
2587 PRO 2.9 0.8 - - - -
2597 GLU* 1.4 76.9 - - - +
2617 LEU* 1.3 58.2 + - - +
2637 GLN 2.7 31.7 - - - +
2647 PRO* 3.4 5.7 - - - +
2667 PHE* 3.9 5.4 - - + -
2677 ILE* 3.6 47.8 - - + -
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Residues in contact with LEU 261 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1557 SER* 4.8 4.3 - - - +
1787 LEU* 5.1 0.9 - - - +
1807 LEU* 3.5 31.0 - - + +
1857 LEU* 4.0 16.4 - - + -
2197 VAL* 5.6 0.9 - - + -
2587 PRO* 2.9 14.4 + - + +
2607 THR* 1.3 78.8 - - - +
2627 PHE* 1.3 63.2 + - + +
2647 PRO* 4.7 1.6 - - - +
2737 GLY* 3.8 2.9 - - - -
2747 ILE* 3.2 52.8 + - + +
3037 THR* 4.1 17.0 - - + +
3047 THR* 6.5 0.2 - - + -
3067 TYR* 4.0 30.1 - - + -
3097 ILE* 4.3 13.9 - - + -
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Residues in contact with PHE 262 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2197 VAL* 3.5 28.7 - - + -
2237 PHE* 3.9 4.0 - + - -
2587 PRO 3.8 14.4 - - - -
2597 GLU* 3.2 2.2 + - - -
2617 LEU* 1.3 78.8 - - + +
2637 GLN* 1.3 73.4 + - - +
2647 PRO* 3.6 8.1 - - - +
2737 GLY* 4.0 4.2 + - - -
2747 ILE* 3.6 27.1 - - + -
2757 HIS* 3.4 39.6 - - + +
3097 ILE* 4.6 10.5 - - + -
3127 ARG* 3.3 51.1 - - + +
3137 MET* 4.2 17.7 - - + -
3167 GLU* 4.0 2.7 - - + -
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Residues in contact with GLN 263 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2597 GLU* 2.7 63.9 + - - +
2607 THR* 2.7 23.8 - - - +
2627 PHE* 1.3 93.2 - - - +
2647 PRO* 1.3 59.8 - - - +
2657 SER* 3.1 20.1 + - - +
2667 PHE* 3.5 26.0 + - + +
3127 ARG* 3.4 9.9 + - - +
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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