Contacts of the strand formed by residues 152 - 158 (chain B) in PDB entry 6VSU
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 LEU 152 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ALA* 3.9 14.4 - - - +
51B LYS* 4.4 4.5 - - + +
52B GLY* 4.1 12.3 - - - +
55B VAL* 4.1 23.8 - - + -
64B SER* 3.2 14.1 - - - +
66B SER* 4.1 15.5 - - - +
115B THR* 4.0 16.6 - - - +
117B VAL* 4.6 4.5 - - + -
146B VAL* 3.3 23.7 - - + +
147B MET* 4.0 20.3 - - - +
149B GLU* 2.9 42.6 + - + +
151B PRO* 1.3 75.6 - - - +
153B ARG* 1.3 61.2 + - - +
154B PRO* 4.5 0.6 - - - +
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Residues in contact with ARG 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LYS 4.6 6.9 + - - -
63B ALA* 3.5 27.9 - - + +
64B SER 2.8 10.8 + - - +
65B THR* 3.5 5.2 - - - +
66B SER 2.8 26.7 + - - -
146B VAL* 4.6 1.8 - - - -
151B PRO 3.9 6.7 + - - +
152B LEU* 1.3 75.3 - - - +
154B PRO* 1.3 73.2 - - + +
305B ASP* 2.9 31.3 + - - -
306B VAL 3.0 25.9 + - - -
307B VAL* 3.9 21.9 - - - +
340B ILE* 3.6 19.8 + - + +
342B LYS* 3.7 13.5 - - - +
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Residues in contact with PRO 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B SER 3.5 7.2 - - - +
68B LEU* 5.5 2.7 - - + -
143B VAL* 4.1 20.4 - - + -
146B VAL* 4.3 18.4 - - + -
147B MET* 3.8 29.4 - - + -
152B LEU 4.5 0.4 - - - +
153B ARG* 1.3 85.6 - - + +
155B LEU* 1.3 59.4 + - - +
156B VAL* 4.0 14.0 - - + +
167B VAL* 5.7 1.3 - - + -
171B VAL* 4.4 9.6 - - + -
266B TYR* 5.4 0.2 - - - -
307B VAL 3.7 13.2 - - - +
308B GLY* 3.2 5.3 - - - -
309B ALA 3.1 21.7 + - - +
340B ILE* 4.7 2.1 - - - +
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B THR* 3.6 30.5 - - + -
66B SER 3.0 6.2 + - - +
67B LEU* 3.3 12.9 - - + +
68B LEU 3.1 20.5 + - - -
153B ARG 3.5 0.4 + - - -
154B PRO* 1.3 71.6 - - - +
156B VAL* 1.3 73.6 + - - +
157B LEU* 3.8 16.9 + - + -
309B ALA* 3.3 17.5 - - + +
310B ASP 4.8 0.2 - - - -
311B VAL* 4.5 9.6 - - + +
333B VAL* 3.5 39.5 - - + +
336B LEU* 3.6 19.3 - - + -
337B ALA 3.9 1.3 - - - +
340B ILE* 4.4 4.7 - - + -
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Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 3.2 21.8 - - + +
70B VAL* 3.7 23.1 - - + -
143B VAL* 4.4 11.2 - - + -
154B PRO* 4.6 8.3 - - + -
155B LEU* 1.3 78.6 - - - +
157B LEU* 1.3 60.9 + - - +
163B ILE* 3.9 20.6 - - + -
167B VAL* 3.7 34.8 - - + -
309B ALA 2.7 12.7 + - - +
310B ASP* 3.1 10.2 - - + +
311B VAL 3.0 26.0 + - - -
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Residues in contact with LEU 157 (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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67B LEU* 4.4 19.5 - - + -
68B LEU 2.9 10.7 + - - +
69B GLY* 3.4 3.9 - - - -
70B VAL* 2.9 31.5 + - - +
86B PRO* 3.5 38.6 - - + +
89B ILE* 4.2 19.7 - - + -
90B ARG* 4.3 22.2 - - + +
155B LEU* 4.0 9.6 - - + -
156B VAL* 1.3 76.2 - - - +
158B GLY* 1.3 64.6 + - - +
311B VAL* 3.8 4.7 - - + -
333B VAL* 3.5 36.1 - - + -
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Residues in contact with GLY 158 (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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70B VAL 4.0 0.2 - - - -
85B ALA* 3.3 22.8 - - - +
86B PRO* 3.5 7.5 - - - +
89B ILE* 4.1 4.3 - - - +
156B VAL 3.9 2.2 + - - -
157B LEU* 1.3 77.5 - - - +
159B GLY* 1.3 71.6 + - - -
163B ILE* 3.5 16.5 - - - +
311B VAL 2.9 20.1 + - - +
312B VAL* 4.1 2.6 - - - +
313B GLU 4.9 1.0 + - - -
314B PHE* 5.5 0.5 + - - +
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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