Contacts of the strand formed by residues 36 - 41 (chain T) in PDB entry 5M32
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 ALA 36 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34T SER 5.1 0.2 - - - +
35T THR* 1.3 77.3 - - - +
37T ILE* 1.3 62.5 + - - +
48T GLY 3.3 10.1 - - - +
49T VAL* 3.8 19.7 - - + -
65T ARG* 4.7 0.2 - - - +
76T ALA* 4.2 17.0 - - + -
77T VAL 3.8 18.6 - - - +
136T MET* 3.3 22.8 - - - +
165T ILE* 3.0 20.4 + - + +
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Residues in contact with ILE 37 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35T THR* 4.8 4.7 - - - -
36T ALA* 1.3 78.9 - - - +
38T GLY* 1.3 58.5 + - - +
39T ILE* 3.8 19.5 - - + +
46T VAL 5.1 0.2 - - - +
47T PHE* 3.5 3.3 - - - +
48T GLY 2.8 35.8 + - - +
76T ALA* 5.2 0.5 - - - +
136T MET* 4.4 1.8 - - - -
163T CYS 3.9 4.0 - - - -
164T ALA* 3.7 21.8 - - + +
172T ALA* 4.2 12.6 - - + -
176T ILE* 4.0 15.0 - - + -
193T VAL* 3.7 38.1 - - + -
196T ILE* 4.2 14.8 - - + -
197T ILE* 3.7 24.4 - - + +
200T VAL* 6.0 0.4 - - + -
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Residues in contact with GLY 38 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37T ILE* 1.3 75.7 - - - +
39T ILE* 1.3 63.0 + - - -
40T ARG 4.1 0.2 - - - -
46T VAL 3.4 7.0 - - - -
47T PHE* 4.2 8.1 - - - -
136T MET* 3.9 16.2 - - - -
148T LEU* 4.1 9.3 - - - +
161T TRP 3.6 2.3 - - - +
162T GLY* 3.3 26.3 - - - -
163T CYS 3.1 11.9 + - - +
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Residues in contact with ILE 39 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37T ILE* 3.8 24.5 - - + -
38T GLY* 1.3 76.4 - - - +
40T ARG* 1.3 65.4 + - - +
45T VAL* 3.6 3.0 - - - +
46T VAL 2.9 36.3 + - - +
161T TRP 3.8 2.0 - - - -
162T GLY* 4.4 0.4 - - - -
176T ILE* 4.2 21.8 - - + -
179T LEU* 4.7 18.4 - - + -
181T MET* 3.7 19.7 - - + +
189T ILE* 3.7 29.9 - - + +
193T VAL* 3.8 15.9 - - + -
196T ILE* 4.3 17.3 - - + -
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Residues in contact with ARG 40 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38T GLY 4.1 0.2 - - - -
39T ILE* 1.3 75.8 - - - +
41T CYS* 1.3 68.8 + - - +
44T GLY 4.0 2.9 - - - -
45T VAL* 4.3 4.9 - - + +
145T GLY* 4.5 3.4 - - - -
146T ALA* 2.9 47.7 + - + +
147T GLN* 4.0 25.4 + - - +
148T LEU* 3.7 17.7 + - + +
159T GLY 6.1 0.2 - - - -
160T TYR 3.7 13.8 + - - -
161T TRP* 2.8 62.7 + - + +
181T MET* 3.3 24.4 - - - +
62U ASP* 3.8 19.6 + - - -
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Residues in contact with CYS 41 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40T ARG* 1.3 78.6 - - - +
42T LYS* 1.3 64.8 + - - +
43T ASP* 3.3 22.4 - - - -
44T GLY 2.9 32.4 + - - +
146T ALA* 3.3 11.6 - - - +
161T TRP* 5.7 3.6 - - - -
181T MET 4.2 11.9 - - - +
182T LYS 4.4 2.7 - - - +
184T MET* 3.3 20.4 - - + +
186T CYS* 3.5 21.5 - - - -
189T ILE* 3.7 15.0 - - + -
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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