Contacts of the strand formed by residues 732 - 736 (chain M) in PDB entry 2W4G
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 ILE 732 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C LEU* 3.9 1.3 - - + -
107C LEU* 3.2 30.3 - - + -
111C LEU* 5.6 3.4 - - + -
139C TYR 2.4 7.7 - - - +
142C PHE* 1.2 200.1 + - + +
143C VAL* 1.7 8.4 - - - +
146C ILE* 2.0 47.3 - - + -
729M ALA 2.6 22.7 - - - +
730M SER* 1.3 46.2 + - - +
731M ALA 1.9 35.1 - - - -
736M GLN* 3.5 4.3 - - + +
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Residues in contact with PRO 733 (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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130C GLN* 3.1 2.2 - - - +
141C ALA* 0.6 118.0 + - - +
142C PHE* 0.5 267.2 + - + +
143C VAL* 2.2 18.6 - - - +
144C LYS 2.3 2.9 - - - -
145C HIS* 1.3 88.6 - - + +
146C ILE* 2.7 14.8 - - + +
732M ILE* 1.3 1.7 - - - -
734M GLU 1.3 0.4 - - - -
737M PHE 3.1 6.4 + - - -
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Residues in contact with GLU 734 (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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140C GLU 0.5 203.8 - - - +
141C ALA* 0.9 170.9 + - + +
142C PHE* 1.8 6.5 - - - +
144C LYS* 0.7 370.5 + - + +
145C HIS* 5.8 0.9 - - + -
733M PRO* 1.3 6.3 - - - +
735M GLY 1.3 31.6 - - - +
738M MET* 1.0 36.5 - - - +
746M LYS* 2.0 4.8 + - - +
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Residues in contact with GLY 735 (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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88C VAL* 4.5 2.2 - - - -
100C GLY 3.0 0.7 - - - +
138C ASN 2.3 0.2 - - - -
139C TYR* 0.7 329.3 + - - +
140C GLU* 1.2 38.4 + - - +
141C ALA 2.1 0.8 - - - +
142C PHE 2.7 2.8 - - - +
143C VAL* 3.3 3.8 - - - +
731M ALA 3.3 8.6 + - - -
732M ILE 3.0 0.2 + - - -
734M GLU* 1.3 60.2 - - - +
736M GLN 1.3 21.5 - - - -
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Residues in contact with GLN 736 (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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102C VAL* 3.3 11.7 - - + -
107C LEU* 2.5 3.7 - - - +
127C MET* 5.7 2.9 - - - +
130C GLN* 4.7 1.7 - - - +
131C GLU* 3.2 10.6 + - - +
137C ILE* 2.4 33.3 - - + +
138C ASN* 0.7 145.0 + - - +
139C TYR* 1.8 14.5 + - - +
142C PHE* 0.5 210.3 - - + -
725M ARG* 2.0 36.1 - - - +
732M ILE* 2.8 7.4 + - + +
735M GLY 1.3 57.0 - - - +
737M PHE* 1.3 43.5 - - - -
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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