Contacts of the strand formed by residues 149 - 154 (chain A) in PDB entry 4CQM
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 GLY 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A SER* 3.3 11.7 - - - -
142A LEU* 3.8 14.8 - - - -
147A CYS 3.7 1.0 + - - -
148A ARG* 1.3 75.4 - - - +
150A SER* 1.3 57.0 + - - -
191A GLY 3.0 10.8 + - - +
192A ILE* 3.3 7.1 - - - +
193A ARG* 2.7 33.6 + - - +
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Residues in contact with SER 150 (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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98A SER 3.0 11.6 + - - -
99A VAL* 3.7 5.1 - - - +
100A VAL 3.3 20.8 + - - +
142A LEU* 4.8 0.8 - - - +
149A GLY* 1.3 72.8 - - - -
151A ILE* 1.3 62.8 + - - +
152A ILE* 3.8 10.6 + - - +
192A ILE* 4.7 0.2 - - - +
193A ARG* 3.3 31.2 + - - +
195A ASN* 5.2 1.6 + - - -
240A LEU* 2.8 25.8 + - - +
241A ALA* 3.7 14.1 - - - -
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Residues in contact with ILE 151 (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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100A VAL* 3.5 26.5 - - + +
102A SER* 5.8 0.2 - - - +
135A THR* 4.0 35.2 - - + +
138A ALA* 4.6 5.2 - - + -
139A ALA* 4.4 10.5 - - + +
142A LEU* 5.0 4.7 - - + -
150A SER* 1.3 74.2 + - - +
152A ILE* 1.3 62.8 + - - +
153A ASN* 3.9 21.3 + - - +
180A THR* 4.9 0.5 - - - +
187A LEU* 4.2 8.3 - - + -
192A ILE* 3.9 26.0 - - + -
193A ARG 2.6 11.3 + - - +
194A CYS* 3.3 17.3 - - + -
195A ASN* 3.1 26.3 + - - +
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Residues in contact with ILE 152 (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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99A VAL* 4.8 0.2 - - + -
100A VAL 2.7 9.3 + - - -
101A VAL* 3.2 21.0 - - + +
102A SER 3.1 22.2 + - - -
150A SER* 4.0 12.8 - - - +
151A ILE* 1.3 77.2 - - - +
153A ASN* 1.3 62.0 + - - +
154A ILE* 4.5 1.8 - - + -
195A ASN* 3.6 4.7 - - + +
197A VAL* 3.7 29.8 - - + -
237A VAL* 3.2 46.7 - - + +
240A LEU* 3.7 16.8 - - + -
241A ALA* 3.6 25.8 - - + +
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Residues in contact with ASN 153 (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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102A SER* 3.7 14.0 + - - +
131A THR* 3.4 18.6 - - + +
135A THR* 3.4 26.8 + - - +
151A ILE* 3.9 14.0 - - - +
152A ILE* 1.3 74.3 - - - +
154A ILE* 1.3 60.6 - - - +
155A SER* 3.2 4.0 + - - -
176A VAL* 3.7 14.5 + - + +
179A LEU* 4.8 1.8 - - - +
180A THR* 2.7 40.1 + - - +
194A CYS* 5.7 0.2 - - - +
195A ASN 3.0 7.7 + - - +
196A SER* 3.3 5.2 - - - -
197A VAL 3.0 22.3 + - - -
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Residues in contact with ILE 154 (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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23A ILE* 4.5 15.3 - - + -
101A VAL* 4.0 9.2 - - + -
102A SER* 3.3 24.9 + - - +
103A CYS* 3.6 26.2 - - + +
131A THR* 5.7 0.9 + - - -
152A ILE* 4.5 0.9 - - + -
153A ASN* 1.3 69.0 - - - +
155A SER* 1.3 69.0 + - - +
173A LYS* 3.4 17.7 + - - +
176A VAL* 4.8 4.6 - - - +
197A VAL* 3.8 24.9 - - + -
199A PRO* 4.1 16.2 - - + -
233A VAL* 4.4 6.1 - - + -
237A VAL* 3.9 24.0 - - + -
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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