Contacts of the helix formed by residues 639 - 644 (chain A) 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 GLY 639 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238 GLY 2.4 26.3 - - - +
248 ASP 2.8 7.0 + - - +
3418 ILE* 4.9 0.8 - - - +
3448 SER* 2.4 38.3 + - - -
3458 ILE* 1.9 18.8 - - - +
3488 SER* 3.0 4.9 - - - -
632A GLY 3.1 0.9 - - - +
633A GLY* 4.0 4.2 - - - -
638A GLY* 1.3 62.8 - - - -
640A LYS* 1.3 55.0 + - - -
641A LYS 3.1 3.1 - - - -
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Residues in contact with LYS 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238 GLY 2.1 24.5 - - - +
3458 ILE* 6.0 1.3 - - + -
3488 SER* 3.6 3.0 + - - -
540A CYS 6.1 0.9 - - - -
600A MLY 3.2 39.0 + - - +
601A ASP 5.0 2.0 + - - -
602A PRO* 5.5 2.8 - - - +
629A GLU 4.1 1.2 - - - +
633A GLY* 4.8 7.9 - - - -
638A GLY 5.8 0.7 - - - +
639A GLY* 1.3 67.8 - - - -
641A LYS* 1.4 53.1 + - - +
643A GLY* 3.4 3.1 + - - -
645A SER* 2.1 60.5 + - - +
646A PHE 2.9 21.6 + - - +
647A GLN* 4.1 8.5 + - + +
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Residues in contact with LYS 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48 GLU* 3.3 54.5 - - + +
58 THR* 5.0 6.8 - - - +
218 PHE* 5.1 0.3 - - - +
228 ALA 2.6 13.4 - - - +
238 GLY* 1.6 14.2 - - - -
3478 ALA 4.7 1.0 + - - -
3488 SER* 1.8 32.2 + - - +
3498 LEU 4.0 8.1 + - - -
3508 SER* 4.3 3.2 - - - +
537A GLU* 5.1 1.8 + - - -
640A LYS* 1.4 70.1 - - - +
642A LYS* 1.2 51.0 + - - -
643A GLY 3.0 2.7 - - - -
644A SER* 2.9 20.1 + - - +
645A SER 3.2 12.1 - - - +
647A GLN* 1.8 77.4 - - + +
651A ALA* 5.0 10.0 - - - +
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Residues in contact with LYS 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98 VAL* 4.3 0.7 - - - -
218 PHE* 2.2 30.6 - - - +
228 ALA* 2.7 6.7 - - - +
238 GLY* 1.0 104.0 - - - +
248 ASP* 1.0 191.1 - - + +
288 ARG* 3.5 3.6 + - - -
3408 TRP* 2.5 49.9 + - + -
3418 ILE* 2.9 8.7 + - - +
3448 SER* 0.7 206.5 - - - +
641A LYS 1.2 35.1 - - - -
643A GLY* 1.3 46.1 - - - -
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Residues in contact with GLY 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238 GLY 2.6 5.5 - - - -
248 ASP* 2.2 22.3 - - - +
288 ARG* 5.2 0.4 - - - -
628A GLY 3.0 4.8 - - - +
629A GLU* 1.9 41.2 + - - -
631A GLU* 4.8 2.2 - - - -
632A GLY* 3.4 3.4 - - - -
642A LYS* 1.3 66.1 - - - +
644A SER* 1.3 73.9 + - - +
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Residues in contact with SER 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48 GLU* 5.0 9.7 - - - +
58 THR* 6.1 4.5 - - - -
625A THR 4.0 0.3 + - - -
628A GLY 3.5 3.1 + - - -
629A GLU* 0.7 139.5 + - - +
641A LYS* 2.9 14.5 + - - +
643A GLY* 1.3 78.6 + - - +
645A SER* 1.3 54.1 - - - +
646A PHE* 4.0 0.7 + - - -
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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