Contacts of the helix formed by residues 176 - 183 (chain B) in PDB entry 5M64
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 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B LYS* 3.7 30.7 + - - -
31B ASP 5.9 0.2 - - - -
174B LYS 4.1 1.0 + - - -
175B MET* 1.3 76.5 - - - +
177B PRO* 1.3 75.2 - - - +
178B TYR* 4.1 3.3 + - - -
179B GLU* 3.0 25.3 + - - +
180B LEU* 3.0 19.4 + - - +
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Residues in contact with PRO 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B PRO* 4.6 11.2 - - + -
29B PRO* 3.3 21.3 - - + +
31B ASP 3.7 17.0 - - - +
32B LYS* 5.4 0.7 - - - -
33B SER* 4.0 24.7 - - - +
175B MET 3.7 2.7 - - - +
176B SER* 1.3 87.1 - - - +
178B TYR* 1.3 59.1 + - - +
180B LEU* 3.2 17.2 + - + +
181B VAL* 3.1 26.1 + - - +
187B SER 3.7 21.2 - - - +
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Residues in contact with TYR 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ASN* 4.6 8.7 - - + -
28B PRO* 3.8 35.5 - - + +
29B PRO 4.7 2.2 - - - +
30B LYS* 3.3 44.2 - - + +
176B SER* 3.2 2.4 - - - +
177B PRO* 1.3 82.1 - - - +
179B GLU* 1.3 61.4 + - - +
181B VAL* 3.2 11.5 + - + +
182B GLN* 3.2 46.3 + - + +
62J ARG* 3.3 30.1 + - - -
69J ARG* 4.2 15.3 + - - -
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Residues in contact with GLU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LYS* 5.0 5.9 + - - -
175B MET* 3.6 17.9 - - + -
176B SER* 3.0 23.2 + - - +
178B TYR* 1.3 75.8 - - - +
180B LEU* 1.3 60.5 + - - +
182B GLN* 2.9 32.1 + - - +
183B HIS* 2.8 63.2 + - + -
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B GLN* 4.3 11.0 - - - +
172B LEU* 3.7 19.1 - - + +
175B MET* 3.6 33.9 - - + +
176B SER 3.0 23.5 + - - +
177B PRO* 3.2 16.1 + - + +
179B GLU* 1.3 77.4 - - - +
181B VAL* 1.3 61.7 + - - +
183B HIS* 3.1 12.1 + - - +
185B GLU* 3.0 31.3 + - + +
186B GLU 3.7 21.8 - - - +
187B SER 5.1 1.6 - - - +
189B GLU* 3.7 25.1 - - + +
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Residues in contact with VAL 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B PRO* 4.0 22.7 - - + -
177B PRO 3.1 15.6 + - - +
178B TYR* 3.2 8.9 + - - +
180B LEU* 1.3 76.5 - - - +
182B GLN* 1.3 61.0 + - + +
183B HIS 3.3 0.7 + - - -
184B LYS* 3.4 9.0 + - - +
185B GLU 4.4 0.9 - - - -
187B SER* 4.3 19.3 - - - -
62J ARG* 3.8 53.0 - - + +
63J TYR* 3.7 24.1 - - + +
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Residues in contact with GLN 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LYS* 5.5 0.4 - - - +
178B TYR* 3.2 40.3 + - + +
179B GLU* 2.9 42.5 + - - +
181B VAL* 1.3 77.1 - - + +
183B HIS* 1.3 60.1 + - - +
184B LYS* 3.4 9.2 + - - +
62J ARG* 6.3 0.4 - - - +
69J ARG* 3.4 51.6 - - + +
33L GLU* 5.1 6.2 - - - +
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Residues in contact with HIS 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B LYS* 5.3 1.4 - - - -
122B TYR* 3.3 56.3 + + + +
123B PRO* 6.0 2.6 - - + +
124B SER* 3.9 5.9 - - - -
172B LEU* 5.4 2.9 - - + -
175B MET* 3.9 22.6 - - + +
179B GLU* 2.8 57.1 + - + +
180B LEU* 3.1 7.5 + - - +
182B GLN* 1.3 78.8 - - + +
184B LYS* 1.3 79.8 + - - +
185B GLU* 3.3 20.2 + - + +
33L GLU* 5.7 2.2 - - - -
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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