Contacts of the strand formed by residues 158 - 164 (chain A) in PDB entry 1CMO
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 GLN 158 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A SER* 3.7 13.4 + - - +
68A PRO* 5.3 1.0 - - - +
69A ASN* 3.7 30.7 + - + +
70A PHE* 3.1 47.0 - - + -
95A GLY* 4.8 7.1 - - - -
97A VAL* 5.8 2.0 - - + -
150A ILE 4.2 0.2 - - - +
151A THR* 3.9 4.0 - - - -
152A VAL* 3.5 27.9 + - + +
156A PRO* 2.8 39.7 + - + +
157A PRO* 1.3 74.0 + - - +
159A VAL* 1.3 62.7 + - - +
160A ALA 4.0 0.3 + - - -
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Residues in contact with VAL 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ASP* 4.3 7.1 - - + +
67A SER* 2.3 41.7 + - - +
150A ILE 4.0 5.4 - - - +
151A THR* 4.8 12.6 - - + +
157A PRO* 4.4 9.4 - - + +
158A GLN* 1.3 75.3 - - - +
160A ALA* 1.3 62.9 + - - +
161A THR* 4.2 16.8 - - + -
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Residues in contact with ALA 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A THR* 4.2 20.2 - - + -
66A ASP 4.9 0.4 - - - +
67A SER 4.9 0.2 - - - +
70A PHE* 4.0 28.3 - - + -
72A CYS* 5.5 1.6 - - - -
91A VAL* 6.1 0.2 - - + -
150A ILE* 2.6 64.7 + - + +
158A GLN 4.0 0.2 + - - -
159A VAL* 1.3 77.5 - - - +
161A THR* 1.3 58.1 + - - +
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Residues in contact with THR 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ARG 4.9 1.2 - - - +
65A THR* 4.3 19.7 - - - +
66A ASP* 3.0 28.6 + - - +
147A THR* 6.0 0.9 - - - -
148A LEU 3.2 13.5 - - - -
149A THR* 4.0 21.3 - - + +
150A ILE* 4.5 1.3 - - - +
151A THR* 6.2 0.4 - - + -
159A VAL* 4.2 19.1 - - + -
160A ALA* 1.3 81.1 - - - +
162A TYR* 1.3 63.4 + - - +
163A HIS* 5.1 6.6 + - - +
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Residues in contact with TYR 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A VAL* 3.8 29.6 - - + -
64A ARG 5.0 4.3 - - - +
65A THR* 5.8 2.5 - - + -
76A PRO* 5.4 9.2 - - + -
77A THR* 3.6 37.5 - - + +
146A PHE* 5.5 1.6 - + - -
147A THR* 3.8 0.7 - - - -
148A LEU* 2.8 62.9 + - + +
161A THR* 1.3 75.2 - - - +
163A HIS* 1.3 63.3 + - - +
164A ARG* 3.0 62.6 + - + +
165A ALA 5.1 3.9 + - - -
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Residues in contact with HIS 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A ASP* 5.9 1.0 + - - -
110A ASP* 5.7 1.6 - - - +
145A SER* 6.5 1.1 - - - -
146A PHE 3.4 11.7 - - - +
147A THR* 4.5 14.8 - - + +
161A THR* 5.1 7.0 + - - +
162A TYR* 1.3 80.2 - - - +
164A ARG* 1.3 79.1 + - - +
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Residues in contact with ARG 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A THR* 5.6 2.9 - - - +
145A SER* 5.6 1.3 - - - -
146A PHE* 3.2 30.2 + - - +
162A TYR* 3.0 48.0 + - + +
163A HIS* 1.3 89.2 + - - +
165A ALA* 1.3 79.4 + - + +
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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