Contacts of the helix formed by residues 627 - 635 (chain M) in PDB entry 3RWR
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 SER 627 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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546M HIS* 5.1 7.0 - - - +
625M LEU 3.3 2.8 + - - -
626M ALA* 1.3 72.0 - - - +
628M PRO* 1.3 74.1 - - - +
629M SER* 4.4 7.2 + - - -
630M LEU* 3.0 33.4 + - - +
631M VAL* 3.0 14.8 + - - +
556Q GLN* 3.7 29.4 - - - +
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Residues in contact with PRO 628 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L GLN 5.0 2.6 - - - +
43L GLN* 5.0 18.6 - - + +
125L LEU* 4.9 15.0 - - + -
626M ALA 3.7 4.0 - - - +
627M SER* 1.3 80.9 - - - +
629M SER* 1.3 58.8 + - - +
630M LEU 2.8 10.7 + - - -
631M VAL* 3.1 9.8 + - + +
632M SER* 3.1 24.8 + - - -
636M ILE* 5.8 0.2 - - - +
556Q GLN* 5.2 4.7 - - + -
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Residues in contact with SER 629 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42L GLN* 4.3 20.1 + - - +
43L GLN* 5.2 10.3 + - - +
627M SER* 3.3 6.9 - - - -
628M PRO* 1.3 79.0 - - - +
630M LEU* 1.3 58.9 + - - +
632M SER* 4.3 3.6 - - - -
633M GLN* 3.9 20.8 + - - +
560Q GLU* 3.6 20.2 + - - -
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Residues in contact with LEU 630 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505M GLU* 3.1 31.0 - - + +
508M LEU* 4.8 0.4 - - + -
509M LEU* 5.7 0.2 - - + -
537M LEU* 3.8 22.2 - - + -
546M HIS* 3.4 24.7 - - + -
626M ALA* 5.6 0.2 - - + -
627M SER* 3.0 20.4 + - - +
628M PRO 2.8 1.0 + - - -
629M SER* 1.3 78.1 - - - +
631M VAL* 1.3 55.1 + - + +
632M SER 2.7 6.6 + - - -
633M GLN* 2.7 42.7 + - + +
634M HIS* 2.9 40.9 + - + +
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Residues in contact with VAL 631 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131L VAL* 5.5 6.1 - - + -
136L ILE* 4.2 20.9 - - + -
537M LEU* 5.9 1.1 - - - -
544M VAL* 3.4 48.9 - - + -
626M ALA* 3.9 10.1 - - + +
627M SER 3.0 17.8 + - - +
628M PRO* 3.8 8.7 - - + +
630M LEU* 1.3 74.8 - - - +
632M SER* 1.3 56.4 + - - +
634M HIS* 4.0 5.4 - - - +
635M LEU* 3.1 25.7 + - + +
636M ILE* 3.3 15.1 + - + +
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Residues in contact with SER 632 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41L LEU 3.0 18.2 + - - -
42L GLN* 3.0 36.3 + - - -
628M PRO 3.1 13.3 + - - -
629M SER 4.3 1.6 - - - -
630M LEU 2.7 1.4 + - - -
631M VAL* 1.3 76.2 - - - +
633M GLN* 1.3 55.6 + - - -
634M HIS 3.2 4.7 - - - -
636M ILE* 3.8 17.9 - - - +
637M ARG* 2.8 44.3 + - - +
638M PRO* 3.0 5.0 - - - +
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Residues in contact with GLN 633 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L GLN* 5.3 3.8 - - - +
509M LEU* 2.9 30.1 - - + +
629M SER 3.9 12.8 + - - +
630M LEU* 2.7 30.2 + - + +
632M SER* 1.3 75.1 - - - +
634M HIS* 1.3 55.8 + - - +
637M ARG* 4.4 15.9 - - - +
638M PRO* 3.8 12.0 - - - +
718M TYR* 4.8 0.2 + - - -
722M THR* 5.4 0.5 - - - +
726M HIS* 3.9 29.8 + - + +
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Residues in contact with HIS 634 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505M GLU* 5.3 1.0 + - - +
508M LEU* 3.2 25.1 - - + +
509M LEU* 3.2 45.4 + - + +
513M TRP* 3.8 7.0 + - + -
526M LYS* 3.6 13.7 - - - -
537M LEU* 3.2 29.6 - - + -
630M LEU* 2.9 43.1 + - + +
631M VAL* 4.6 2.5 - - - +
633M GLN* 1.3 77.8 - - - +
635M LEU* 1.3 60.1 + - + +
638M PRO* 3.0 13.3 - - - +
718M TYR* 2.6 37.0 + - - +
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Residues in contact with LEU 635 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136L ILE* 3.8 31.0 - - + -
140L MET* 5.9 2.0 - - + -
513M TRP* 3.2 48.7 - - + +
524M LEU* 5.8 3.1 - - + -
537M LEU* 5.7 0.2 - - + -
539M SER* 4.5 12.6 - - - +
541M LEU* 5.7 5.2 - - + -
543M GLN 5.8 0.2 - - - +
544M VAL* 4.9 9.2 - - + -
631M VAL* 3.1 20.2 + - + +
634M HIS* 1.3 78.2 - - + +
636M ILE* 1.3 70.0 + - - +
638M PRO* 2.9 2.4 - - - +
639M LEU* 2.7 50.4 + - + +
710M PHE* 4.6 7.9 - - + -
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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