Contacts of the strand formed by residues 172 - 180 (chain B) in PDB entry 3VF0
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 SER 172 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B ARG* 4.2 4.1 - - - +
139B LEU* 5.9 0.2 - - - +
140B PRO 5.1 0.7 + - - -
141B PRO* 3.8 26.4 + - - +
143B LEU 4.4 10.7 + - - -
163B LEU* 4.1 16.8 - - - +
164B VAL 3.8 3.7 + - - -
165B TYR* 3.6 26.3 - - - -
171B GLN* 1.3 73.6 + - - +
173B LYS* 1.3 57.0 + - - +
174B GLY* 3.1 19.7 + - - -
175B TYR 4.5 0.2 + - - -
3001B GOL 3.0 23.3 + - - -
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Residues in contact with LYS 173 (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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164B VAL* 2.8 21.5 + - + +
165B TYR 4.1 0.7 - - - -
166B SER* 4.0 17.9 - - - +
171B GLN 4.6 0.2 - - - +
172B SER* 1.3 72.4 - - - +
174B GLY* 1.3 60.7 + - - +
175B TYR* 3.4 32.3 - - + +
219B HIS* 3.0 42.9 + - - +
220B SER 4.8 2.0 + - - +
272B ALA 4.7 3.4 + - - -
276B GLU* 2.8 42.3 + - - +
296B PHE* 3.3 47.9 + - + +
3001B GOL 4.0 14.9 - - - -
3007B GOL 3.9 1.0 - - - -
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Residues in contact with GLY 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ASN* 3.3 9.4 + - - -
139B LEU* 2.8 51.0 + - - -
141B PRO* 4.7 7.0 - - - -
172B SER* 3.1 15.6 + - - -
173B LYS* 1.3 79.3 - - - +
175B TYR* 1.3 60.0 + - - +
296B PHE 5.4 1.1 - - - +
3001B GOL 5.0 4.5 - - - -
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Residues in contact with TYR 175 (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 CYS* 4.0 7.4 - - - -
136B VAL 3.2 13.5 - - - +
137B ALA* 3.7 14.6 - - + -
139B LEU* 3.8 7.3 - - - +
163B LEU* 3.8 4.3 - - - +
164B VAL* 3.1 50.0 + - + +
172B SER* 4.5 0.8 + - - -
173B LYS* 3.4 29.7 - - + +
174B GLY* 1.3 79.6 - - - +
176B GLY* 1.3 60.8 + - - +
177B PHE* 4.3 2.0 - + - -
218B LEU 2.6 29.4 + - - -
219B HIS* 3.3 4.3 - - - -
220B SER* 3.1 17.8 + - - -
296B PHE* 3.7 24.2 - + + -
297B CYS 4.0 9.6 - - - -
299B PRO* 3.5 25.1 - - + -
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Residues in contact with GLY 176 (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 CYS* 3.4 6.9 - - - -
136B VAL 2.9 32.3 + - - +
139B LEU* 3.9 2.2 - - - +
148B PHE* 3.6 16.2 - - - -
162B PHE 3.2 13.0 - - - -
163B LEU* 4.0 3.1 - - - -
164B VAL 4.4 0.7 - - - -
175B TYR* 1.3 76.0 - - - +
177B PHE* 1.3 67.8 + - - -
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Residues in contact with PHE 177 (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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133B LEU* 4.0 19.5 - - + -
134B LEU 3.3 16.2 - - - -
135B CYS* 3.6 22.4 - - + -
148B PHE* 3.6 5.7 - - - -
160B ARG 3.8 1.0 - - - +
161B CYS* 3.3 4.3 - - - -
162B PHE* 2.8 69.6 + + + -
164B VAL* 4.0 14.1 - - + -
175B TYR* 4.3 4.7 - + - -
176B GLY* 1.3 75.9 - - - -
178B ALA* 1.3 59.9 + - - +
208B THR* 3.7 13.9 - - + -
213B LEU* 3.8 23.6 - - + -
218B LEU* 3.7 16.4 - - + -
299B PRO* 3.7 29.4 - - + -
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Residues in contact with ALA 178 (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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132B ALA 3.6 1.7 - - - +
133B LEU* 3.5 2.6 - - - -
134B LEU* 2.8 44.9 + - + +
136B VAL* 5.0 3.1 - - + +
148B PHE* 4.6 2.6 - - + -
152B VAL* 3.9 28.0 - - + -
158B LEU* 3.9 18.2 - - + -
160B ARG 3.5 4.5 - - - -
161B CYS* 4.6 0.4 - - - +
176B GLY 4.4 0.2 + - - -
177B PHE* 1.3 73.6 - - - +
179B GLU* 1.3 58.2 + - - +
180B TYR* 4.1 12.6 - - + +
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Residues in contact with GLU 179 (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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57B ASN 4.6 1.2 - - - +
58B ARG* 4.5 6.8 + - - +
130B THR* 4.1 13.0 + - - +
132B ALA* 3.2 15.3 + - + +
133B LEU* 3.8 21.5 + - + +
158B LEU* 3.5 4.5 - - - +
159B GLU* 2.7 39.9 + - + +
160B ARG* 2.7 66.8 + - + +
178B ALA* 1.3 74.1 - - - +
180B TYR* 1.3 66.4 + - - +
210B ALA* 3.8 9.0 - - - +
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Residues in contact with TYR 180 (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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60B LYS* 4.9 1.2 + - - -
130B THR* 6.1 0.3 - - - -
132B ALA* 3.1 23.6 + - - +
134B LEU* 4.1 5.2 - - + -
152B VAL* 2.5 42.7 + - - +
155B PHE* 4.1 2.9 - - + -
156B GLY 3.9 20.4 - - - -
157B SER 3.3 15.3 - - - +
158B LEU* 3.7 15.9 - - + -
159B GLU* 4.1 6.5 - - - +
178B ALA* 4.1 15.4 - - + +
179B GLU* 1.3 81.7 - - - +
181B MET* 1.3 64.1 + - - +
182B LYS 3.3 18.2 - - - +
185B SER* 3.6 17.9 - - - -
186B ALA* 3.5 21.3 - - + -
189B ALA* 3.4 32.8 - - + +
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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