Contacts of the helix formed by residues 685 - 694 (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 GLU 685 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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658M HIS* 3.9 5.2 - - - -
682M GLU* 5.0 3.0 + - - +
683M PRO 4.0 3.1 + - - +
684M PHE* 1.3 85.7 - - - +
686M GLU* 1.3 67.1 + - - +
687M ASN* 4.4 8.1 - - + +
688M SER* 2.5 52.6 + - - +
689M PHE* 3.2 5.5 + - - +
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Residues in contact with GLU 686 (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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651M ARG* 6.3 0.4 - - - -
654M ALA* 3.6 34.1 - - + +
655M THR* 5.1 3.3 - - - -
658M HIS* 3.1 35.4 + - - -
684M PHE* 3.7 9.7 - - - -
685M GLU* 1.3 72.9 - - - +
687M ASN* 1.3 74.8 + - - +
688M SER 3.0 0.2 + - - -
689M PHE* 3.1 7.8 + - - +
690M LEU* 3.0 27.2 - - + +
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Residues in contact with ASN 687 (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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685M GLU* 3.5 8.6 - - + +
686M GLU* 1.3 80.2 - - - +
688M SER* 1.3 65.8 + - - +
690M LEU* 3.4 9.1 + - - +
691M GLU* 3.3 29.9 + - - +
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Residues in contact with SER 688 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682M GLU* 5.3 3.5 + - - -
685M GLU* 2.5 51.3 + - - +
687M ASN* 1.3 76.9 - - - +
689M PHE* 1.3 66.7 + - - +
690M LEU 2.9 1.7 + - - -
691M GLU* 3.0 17.7 + - - +
692M GLN* 2.9 40.1 + - - +
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Residues in contact with PHE 689 (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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149L GLN* 3.8 24.5 - - + -
152L GLU* 3.4 37.9 - - + -
153L LEU* 3.5 36.1 - - + -
156L LEU* 6.1 5.6 - - + -
650M VAL* 5.3 1.3 - - + -
654M ALA* 6.2 0.2 - - + -
684M PHE* 4.0 17.5 - + + -
685M GLU 4.0 5.4 - - - +
686M GLU 3.1 7.7 + - - +
688M SER* 1.3 81.6 + - - +
690M LEU* 1.3 73.2 + - + +
692M GLN* 3.8 6.8 - - + +
693M PHE* 2.9 35.0 + + + +
696M GLU* 6.2 0.2 - - - -
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Residues in contact with LEU 690 (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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149L GLN* 4.3 20.2 - - - +
647M GLN* 6.1 0.9 - - - +
650M VAL* 5.4 9.4 - - + -
684M PHE* 6.3 0.2 - - + -
686M GLU* 3.0 35.9 - - + +
687M ASN* 3.6 10.1 - - - +
688M SER 2.9 4.0 + - - -
689M PHE* 1.3 85.9 - - + +
691M GLU* 1.3 55.0 + - - +
693M PHE* 2.8 6.6 + - - +
694M MET* 2.6 58.3 + - + +
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Residues in contact with GLU 691 (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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687M ASN* 3.3 23.4 + - - +
688M SER* 3.0 23.0 + - - +
690M LEU* 1.3 76.6 - - - +
692M GLN* 1.3 61.5 + - + +
694M MET* 3.7 9.6 + - - +
695M ILE* 2.9 37.0 - - + +
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Residues in contact with GLN 692 (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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688M SER* 2.9 35.9 + - - +
689M PHE* 3.8 7.1 - - + +
690M LEU 2.9 0.2 + - - -
691M GLU* 1.3 79.5 - - + +
693M PHE* 1.3 61.1 + - - +
695M ILE* 3.2 9.4 + - - +
696M GLU* 2.9 46.6 + - - +
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Residues in contact with PHE 693 (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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145L ALA 3.8 17.7 - - - -
146L LEU* 5.6 0.4 - - - -
148L CYS* 4.2 14.4 - - + -
149L GLN* 3.8 44.9 - - + -
152L GLU* 5.2 8.7 - - + -
689M PHE* 2.9 32.2 + + + +
690M LEU* 2.8 3.9 + - - +
692M GLN* 1.3 72.0 - - - +
694M MET* 1.3 58.7 + - + +
695M ILE 2.7 15.9 + - - -
696M GLU* 2.9 22.1 + - + +
697M LYS* 3.6 21.8 - - + -
698M LEU* 3.2 50.6 + - + -
701M ALA* 4.2 3.1 - - + -
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Residues in contact with MET 694 (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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149L GLN* 4.1 21.5 - - - +
217L LEU* 4.2 29.4 - - + +
220L ALA* 5.5 3.4 - - - -
690M LEU* 2.6 48.5 + - + +
691M GLU* 3.8 11.4 - - - +
692M GLN 3.3 0.4 - - - -
693M PHE* 1.3 72.2 - - + +
695M ILE* 1.3 62.8 + - + +
698M LEU* 3.4 48.5 - - + +
699M PRO* 4.3 4.0 - - - +
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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