Contacts of the strand formed by residues 133 - 142 (chain A) in PDB entry 4F9P
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 ILE 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A LYS 5.8 1.6 - - - +
128A TYR* 4.3 15.3 - - + +
132A GLY* 1.3 71.2 - - - -
134A HIS* 1.3 62.9 + - - +
135A LEU* 3.7 2.8 + - + +
179A VAL 3.8 0.2 - - - +
180A ILE* 3.3 1.1 - - - -
181A MET* 2.7 45.0 + - + +
212A PHE 5.5 6.3 - - - +
213A PHE* 5.9 6.7 - - - +
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Residues in contact with HIS 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A VAL* 4.2 1.9 - - - -
126A LYS* 3.2 35.2 + - + +
127A GLY 3.2 26.2 + - - +
128A TYR* 4.5 2.0 - - - +
129A LYS* 4.5 12.1 - - + +
132A GLY 3.6 1.6 + - - +
133A ILE* 1.3 74.1 - - - +
135A LEU* 1.3 59.8 + - - +
178A SER* 6.3 2.5 - - - -
179A VAL 3.9 6.1 - - - +
180A ILE* 4.4 5.8 - - + +
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Residues in contact with LEU 135 (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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123A VAL* 6.0 3.4 - - + -
124A ASP 3.5 8.1 - - - +
125A VAL* 5.5 1.8 - - - -
133A ILE* 3.7 3.3 + - + +
134A HIS* 1.3 76.6 - - - +
136A GLU* 1.3 61.2 - - - +
150A TRP* 3.4 20.4 - - + -
178A SER* 3.4 3.0 - - - -
179A VAL 3.0 35.7 + - - +
181A MET* 5.8 5.2 - - + -
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Residues in contact with GLU 136 (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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122A HIS 3.4 1.9 - - - +
123A VAL* 3.3 6.3 - - - -
124A ASP* 2.8 50.1 + - + +
126A LYS* 5.7 5.6 - - + -
134A HIS 4.4 0.2 - - - -
135A LEU* 1.3 75.2 - - - +
137A CYS* 1.3 61.5 + - - +
138A ARG* 5.3 0.8 - - + +
150A TRP* 4.1 3.6 - - - -
176A ALA* 6.3 0.7 - - + -
177A ALA 3.3 8.7 - - - +
178A SER* 4.2 11.4 - - - -
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Residues in contact with CYS 137 (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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121A LEU* 4.6 16.2 - - - -
122A HIS 3.6 5.4 - - - -
123A VAL* 4.8 3.1 - - - +
136A GLU* 1.3 73.6 - - - +
138A ARG* 1.3 62.5 + - - +
150A TRP* 3.6 15.3 - - + +
175A VAL 4.8 0.4 - - - -
176A ALA* 3.2 9.7 - - - +
177A ALA* 2.6 39.1 + - + +
191A CYS* 2.0 49.6 - - + -
204A ALA* 5.4 2.7 - - - -
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Residues in contact with ARG 138 (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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120A ASP 4.5 0.5 - - - +
121A LEU* 3.7 1.8 - - - -
122A HIS* 2.8 60.3 + - + +
124A ASP* 6.5 1.1 - - + -
136A GLU* 5.3 0.7 - - + +
137A CYS* 1.3 78.7 - - - +
139A SER* 1.3 62.9 + - - +
175A VAL 3.7 5.6 - - - -
176A ALA* 4.5 7.9 - - + -
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Residues in contact with SER 139 (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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119A SER* 3.5 23.8 - - - -
120A ASP 5.4 0.7 - - - -
121A LEU* 3.6 19.1 - - - -
138A ARG* 1.3 77.9 - - - +
140A THR* 1.3 62.8 + - - +
142A TRP* 3.7 15.9 - - - -
174A ALA* 3.3 4.0 - - - +
175A VAL* 2.9 33.2 + - - +
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Residues in contact with THR 140 (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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118A GLY* 3.5 1.0 - - - -
119A SER* 3.0 40.6 + - - -
139A SER* 1.3 77.4 - - - +
141A GLY* 1.3 72.2 + - - +
142A TRP* 3.4 3.6 - - - -
172A LEU* 5.0 3.5 - - - +
173A TYR 3.4 9.3 + - - -
174A ALA* 4.0 14.9 - - - +
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Residues in contact with GLY 141 (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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116A ALA* 3.7 9.2 - - - +
117A LEU 3.7 20.3 - - - +
118A GLY* 4.3 0.4 - - - -
140A THR* 1.3 83.5 + - - +
142A TRP* 1.3 60.5 + - - +
143A TYR* 3.7 3.2 + - - -
172A LEU* 3.8 21.7 - - - +
173A TYR 3.0 4.9 + - - -
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Residues in contact with TRP 142 (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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116A ALA 4.0 6.7 - - - -
117A LEU* 3.8 29.6 - - + -
118A GLY* 3.0 37.5 - - - -
119A SER 4.0 1.0 + - - -
121A LEU* 4.9 1.1 - - + +
139A SER* 3.7 28.9 - - - -
140A THR 3.8 12.1 - - - -
141A GLY* 1.3 74.6 - - - +
143A TYR* 1.3 64.2 + - - +
144A PRO 4.2 4.7 - - - +
146A PRO* 4.2 22.7 - - + -
172A LEU* 5.5 0.2 - - - -
173A TYR* 3.0 47.7 + - + +
175A VAL* 5.5 9.0 - - + -
193A ILE* 3.9 33.9 - - + +
195A SER* 4.1 24.7 - - - -
200A LEU 5.5 0.7 - - - -
201A GLU* 5.3 2.5 - - - -
202A LYS* 4.1 22.2 - - + -
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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