Contacts of the helix formed by residues 631 - 636 (chain D) in PDB entry 5MS0
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 TYR 631 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509D GLY* 4.3 13.5 - - - +
627D THR* 3.8 18.2 + - - +
628D GLY 3.9 2.4 + - - +
630D ALA* 1.3 76.3 - - + +
632D ALA* 1.3 58.4 + - - +
633D ALA 3.3 1.3 - - - -
634D ARG* 3.1 16.0 + - + +
635D SER* 2.9 27.2 + - - -
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Residues in contact with ALA 632 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806C PRO* 3.9 25.5 - - + +
505D ASP* 3.6 24.0 - - + +
508D LEU* 4.6 5.6 - - + -
509D GLY* 4.2 14.1 - - - +
628D GLY 3.7 8.5 + - - +
629D PHE* 4.2 7.4 - - - +
630D ALA 3.3 1.0 - - - -
631D TYR* 1.3 78.9 - - - +
633D ALA* 1.3 52.6 + - - +
635D SER* 3.9 3.0 - - - +
636D GLY* 2.8 30.3 + - - -
637D ALA* 4.2 2.9 + - - +
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Residues in contact with ALA 633 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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805C MET* 5.4 6.7 - - + -
806C PRO 3.3 22.1 + - - +
807C TRP* 3.3 18.8 + - - +
629D PHE 4.8 0.2 + - - -
630D ALA 3.8 8.0 + - - +
631D TYR 3.3 0.2 - - - -
632D ALA* 1.3 74.2 - - - +
634D ARG* 1.3 63.1 + - - +
635D SER 3.3 1.4 + - - -
636D GLY* 3.6 12.0 + - - +
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Residues in contact with ARG 634 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1222C GLU* 5.0 10.4 + - - +
630D ALA 4.1 2.3 + - - +
631D TYR* 3.1 26.6 + - + +
633D ALA* 1.3 78.6 - - - +
635D SER* 1.3 58.2 + - - +
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Residues in contact with SER 635 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1222C GLU* 3.9 21.4 - - - +
1223C ARG* 4.7 4.0 - - - +
508D LEU 5.6 0.4 - - - -
509D GLY* 5.1 4.7 - - - -
512D TYR* 4.7 20.4 - - - -
631D TYR 2.9 13.6 + - - -
632D ALA* 3.9 5.8 - - - -
633D ALA 4.0 0.4 - - - -
634D ARG* 1.3 79.6 - - - +
636D GLY* 1.3 64.1 + - - +
637D ALA* 4.6 8.5 - - - -
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Residues in contact with GLY 636 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804C PHE 5.7 1.1 - - - -
805C MET* 5.3 12.1 - - - -
806C PRO 5.9 0.2 - - - -
1222C GLU 5.5 1.1 - - - -
1223C ARG* 4.4 17.5 - - - +
1225C VAL* 5.1 2.8 - - - +
632D ALA 2.8 20.9 + - - -
633D ALA* 3.6 11.5 + - - -
635D SER* 1.3 75.2 - - - +
637D ALA* 1.3 58.2 + - - +
638D SER* 2.9 13.1 + - - -
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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