Contacts of the strand formed by residues 135 - 142 (chain A) in PDB entry 3CFV
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 ASN 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A MSE 2.8 31.0 + - + +
134A GLN* 1.3 81.7 + - - +
136A PRO* 1.3 62.1 - - - +
137A HIS* 2.9 53.7 + - - -
138A ILE* 2.9 41.2 + - + +
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Residues in contact with PRO 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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49A LEU* 4.3 7.0 - - + +
50A PRO* 3.6 33.7 - - + -
51A GLU* 3.7 22.4 - - - +
131A TYR* 3.7 23.2 - - + +
132A MSE 3.0 10.3 - - - +
133A PRO 4.2 7.6 - - - +
134A GLN 4.0 5.6 - - - +
135A ASN* 1.3 91.1 - - - +
137A HIS* 1.3 58.3 + - + +
138A ILE 3.2 2.3 + - - +
139A ILE* 4.4 1.7 - - - +
153A TYR* 3.9 9.9 - - - -
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Residues in contact with HIS 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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51A GLU* 5.5 0.2 + - - -
135A ASN* 2.9 40.6 + - - -
136A PRO* 1.3 78.0 - - + +
138A ILE* 1.3 58.4 + - + +
139A ILE* 4.0 0.8 + - - +
151A PHE 3.6 1.0 - - - +
152A ASP* 3.1 31.5 + - - +
153A TYR* 3.1 65.7 + - + +
154A THR* 3.5 20.9 - - + +
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Residues in contact with ILE 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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131A TYR* 3.4 3.3 - - - -
132A MSE 2.7 55.2 + - + +
135A ASN* 2.9 37.8 + - + +
136A PRO 3.2 0.2 - - - -
137A HIS* 1.3 84.5 - - - +
139A ILE* 1.3 60.8 + - - +
140A ALA 4.3 0.4 + - - -
150A VAL* 3.8 25.4 - - + -
151A PHE 3.3 2.9 - - - +
152A ASP* 4.5 13.2 - - + +
184A TRP* 4.3 11.2 - - + -
206A ILE* 4.7 7.2 - - + -
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Residues in contact with ILE 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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66A VAL* 4.3 23.6 - - + -
78A LEU* 4.1 28.3 - - + -
80A VAL* 4.3 9.2 - - + -
129A ALA* 4.1 8.7 - - + -
130A ARG 3.6 16.8 - - - +
131A TYR* 4.3 11.9 - - + -
136A PRO 4.4 4.5 - - - +
137A HIS 4.5 0.9 - - - -
138A ILE* 1.3 80.1 - - - +
140A ALA* 1.3 72.1 + - - +
149A LEU 4.0 0.2 - - - +
150A VAL* 3.5 2.1 - - - -
151A PHE* 2.7 46.0 + - + +
153A TYR* 3.8 30.7 - - + -
184A TRP* 4.6 1.8 - - - -
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Residues in contact with ALA 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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129A ALA* 3.4 2.9 - - - -
130A ARG 3.0 28.9 + - - -
139A ILE* 1.3 75.4 - - - +
141A THR* 1.3 63.1 + - - +
148A VAL* 5.5 1.1 - - + -
149A LEU 3.2 10.1 - - - +
150A VAL* 4.3 3.4 - - + +
182A LEU* 3.8 13.2 - - + -
184A TRP* 3.5 32.6 - - + +
192A LEU* 3.9 20.6 - - + -
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Residues in contact with THR 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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78A LEU* 5.2 5.2 - - - -
122A HIS* 3.1 26.8 - - + +
126A VAL* 3.3 18.6 - - - +
128A ARG 3.2 7.4 - - - -
129A ALA* 4.5 4.5 - - - -
139A ILE 5.1 0.2 - - - -
140A ALA* 1.3 75.7 - - - +
142A LYS* 1.3 65.2 + - - +
143A THR* 3.9 1.2 + - - +
148A VAL* 3.6 5.1 - - - +
149A LEU* 2.8 46.1 + - + +
151A PHE* 3.4 36.6 - - + -
182A LEU* 3.9 2.0 - - - +
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Residues in contact with LYS 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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125A GLU 3.8 1.0 - - - +
126A VAL 3.8 0.7 - - - -
127A ASN* 2.9 36.0 + - + +
128A ARG* 2.8 14.0 + - + +
141A THR* 1.3 76.9 + - - +
143A THR* 1.3 61.7 + - - +
146A SER 5.7 0.8 + - - -
148A VAL* 3.7 22.0 - - + +
175A HIS* 4.1 7.3 + - - -
177A LYS 5.4 0.6 + - - -
178A GLU 4.8 0.4 - - - -
179A GLY* 3.3 41.7 - - - +
180A TYR 3.8 11.4 - - - +
181A GLY 3.8 4.9 - - - +
182A LEU* 3.6 24.5 - - + -
194A SER* 2.4 34.6 + - - +
195A ALA 2.7 17.9 + - - -
196A SER* 4.5 1.6 - - - -
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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