Contacts of the strand formed by residues 135 - 142 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132B MSE 2.9 31.5 + - + +
134B GLN* 1.3 82.3 + - - +
136B PRO* 1.3 63.3 - - - +
137B HIS* 3.0 47.8 + - - -
138B ILE* 2.9 40.4 + - + +
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Residues in contact with PRO 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LEU* 4.0 10.4 - - + +
50B PRO* 3.8 34.3 - - + -
51B GLU* 3.8 22.2 - - - +
131B TYR* 3.7 22.1 - - + +
132B MSE 3.2 7.8 - - - +
133B PRO 4.3 9.0 - - - +
134B GLN 4.1 4.3 - - - +
135B ASN* 1.3 89.4 - - - +
137B HIS* 1.3 59.3 + - + +
138B ILE 3.2 3.7 + - - +
139B ILE* 4.1 2.6 - - - +
153B TYR* 4.1 6.0 - - - +
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Residues in contact with HIS 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ASN* 3.0 39.1 + - - -
136B PRO* 1.3 79.0 - - + +
138B ILE* 1.3 58.7 + - + +
139B ILE* 4.5 0.4 - - - +
151B PHE 3.5 1.4 - - - +
152B ASP* 3.2 32.8 + - - -
153B TYR* 3.1 66.4 + + + +
154B THR* 3.7 19.6 - - + +
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Residues in contact with ILE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B TYR* 3.5 4.0 - - - +
132B MSE 2.9 51.1 + - + -
135B ASN* 2.9 33.9 + - - +
137B HIS* 1.3 84.7 - - - +
139B ILE* 1.3 62.3 + - - +
150B VAL* 4.1 23.1 - - + -
151B PHE 3.4 3.4 - - - +
152B ASP* 4.7 14.4 - - + +
184B TRP* 4.1 19.9 + - + -
206B ILE* 4.5 7.2 - - + -
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Residues in contact with ILE 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B LEU* 5.3 0.2 - - + -
66B VAL* 4.2 25.8 - - + -
78B LEU* 4.2 23.8 - - + -
80B VAL* 4.4 8.5 - - + -
129B ALA* 4.2 12.6 - - + -
130B ARG 3.4 18.6 - - - +
131B TYR* 4.2 7.4 - - + -
136B PRO 4.1 11.0 - - - +
137B HIS 4.5 0.9 - - - -
138B ILE* 1.3 82.2 - - - +
140B ALA* 1.3 70.3 + - - +
149B LEU 3.9 0.2 - - - +
150B VAL* 3.4 2.2 - - - -
151B PHE* 2.8 45.1 + - + +
153B TYR* 4.0 26.7 - - + -
184B TRP* 4.5 2.0 - - - -
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Residues in contact with ALA 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B ALA* 3.3 4.0 - - - -
130B ARG 2.9 31.3 + - - -
139B ILE* 1.3 72.8 - - - +
141B THR* 1.3 62.2 + - - +
148B VAL* 5.4 0.7 - - + -
149B LEU 3.2 9.4 - - - +
150B VAL* 4.4 2.0 - - + +
182B LEU* 3.4 14.2 - - + +
184B TRP* 3.5 30.5 - - + +
192B LEU* 3.6 22.2 - - + -
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Residues in contact with THR 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B LEU* 3.9 37.7 - - + -
122B HIS* 3.2 30.5 - - + -
126B VAL* 4.2 4.3 - - + -
128B ARG 3.1 6.7 - - - -
129B ALA* 4.0 5.8 - - + -
139B ILE* 4.4 1.3 - - + -
140B ALA* 1.3 80.2 - - - +
142B LYS* 1.3 63.4 + - - +
148B VAL* 3.4 9.2 - - - +
149B LEU* 2.8 48.6 + - - +
151B PHE* 3.7 7.7 - - + -
182B LEU* 4.5 1.1 - - - -
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Residues in contact with LYS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B HIS* 4.5 1.0 + - - -
125B GLU 3.7 2.1 - - - +
126B VAL* 3.8 2.1 - - - -
127B ASN* 2.8 47.4 + - + +
128B ARG* 2.9 11.6 + - + +
141B THR* 1.3 73.6 - - - +
143B THR* 1.3 60.8 + - - +
146B SER 5.2 2.0 + - - -
148B VAL* 3.8 21.9 - - + +
175B HIS* 3.9 8.7 + - - -
177B LYS 5.2 1.0 + - - -
178B GLU* 4.6 1.0 - - - +
179B GLY* 3.4 27.4 - - - +
180B TYR 3.8 12.1 - - - +
181B GLY 4.0 4.5 - - - +
182B LEU* 3.7 24.0 - - + -
194B SER* 2.6 29.3 + - - +
195B ALA 2.8 21.6 + - - -
196B SER* 4.5 1.8 - - - -
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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