Contacts of the strand formed by residues 167 - 173 (chain A) in PDB entry 4CYM
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 PHE 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A VAL* 3.8 31.0 - - + -
117A VAL* 4.3 14.6 - - + -
118A LEU* 5.7 0.7 - - + -
121A LYS* 3.6 27.4 - - + -
138A ALA* 3.5 22.2 - - + +
140A LEU* 3.8 25.8 - - + -
161A PHE* 4.0 22.0 - + - -
162A CYS* 2.9 43.5 + - + +
163A LYS* 5.0 1.4 - - - +
165A HIS* 3.5 24.0 - - + -
166A GLY* 1.3 78.1 - - - +
168A ALA* 1.3 63.5 + - - +
169A GLY 3.1 4.5 + - - +
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Residues in contact with ALA 168 (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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137A PRO* 5.1 6.1 - - + -
138A ALA 2.9 20.9 + - - +
139A VAL* 4.7 1.8 - - + -
166A GLY 3.8 3.2 + - - -
167A PHE* 1.3 70.7 - - - +
169A GLY* 1.3 56.4 + - - +
187A PHE* 3.2 20.1 - - + -
191A LYS* 3.7 30.7 - - + -
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Residues in contact with GLY 169 (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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138A ALA 4.0 2.2 + - - -
139A VAL* 4.3 4.2 - - - +
140A LEU* 3.3 18.2 + - - +
162A CYS* 3.5 12.5 - - - -
167A PHE* 3.1 5.0 + - - +
168A ALA* 1.3 80.5 - - - +
170A TRP* 1.3 69.6 + - - +
171A PHE* 5.1 0.2 - - - -
187A PHE* 3.9 15.6 - - - -
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Residues in contact with TRP 170 (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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106A PHE* 6.1 0.2 - + - -
140A LEU* 3.2 22.4 - - + +
142A ALA* 4.4 13.7 - - + -
149A LYS* 5.9 2.2 - - - -
155A PRO* 3.7 42.0 - - + -
158A VAL* 3.1 32.0 - - + +
159A ASP* 2.8 28.0 + - - -
162A CYS* 3.7 23.3 - - + -
169A GLY* 1.3 76.5 - - - +
171A PHE* 1.3 97.1 + - - +
172A GLU* 3.7 33.9 - - + -
163B LYS* 4.4 5.0 + - - -
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Residues in contact with PHE 171 (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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139A VAL* 3.9 18.6 - - + -
140A LEU 3.2 4.4 + - - -
141A LEU* 3.6 5.2 - - + -
142A ALA 2.9 24.4 + - - -
169A GLY* 5.1 0.2 - - - -
170A TRP* 1.3 108.9 - - - +
172A GLU* 1.3 63.3 + - - +
173A THR* 3.4 17.7 + - + +
180A ASN* 4.1 11.7 - - + +
183A GLU* 4.0 10.3 - - + -
184A ALA* 3.6 37.7 - - + -
187A PHE* 3.5 37.7 - + + -
159B ASP* 6.2 1.3 - - + -
160B GLN* 5.6 2.5 - - - -
163B LYS* 3.8 26.0 - - - +
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Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A ILE* 3.5 25.5 - - + +
142A ALA* 3.4 7.4 - - - +
145A CYS* 4.0 19.8 - - + +
149A LYS* 3.6 19.2 + - - -
155A PRO* 5.4 5.3 - - - +
170A TRP* 3.7 25.6 - - + -
171A PHE* 1.3 70.3 - - - +
173A THR* 1.3 58.2 + - - +
179A ILE* 3.7 3.6 - - + +
180A ASN* 2.9 34.2 + - - +
163B LYS* 5.0 2.4 - - - +
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Residues in contact with THR 173 (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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41A ILE* 4.4 2.9 - - - +
141A LEU* 3.9 30.4 - - + +
142A ALA 2.8 9.2 + - - +
143A ASN* 2.7 33.3 + - - +
144A LYS 3.0 22.7 + - - -
145A CYS* 3.1 11.5 + - - -
171A PHE* 3.8 16.2 - - + +
172A GLU* 1.3 78.2 - - - +
174A SER* 1.3 61.7 + - - +
179A ILE 3.2 12.8 - - - +
180A ASN 4.2 10.1 - - - +
181A ILE* 4.3 11.0 - - + -
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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