Contacts of the strand formed by residues 153 - 158 (chain B) in PDB entry 1V2E
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 THR 153 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B GLU* 3.5 13.1 + - + +
106B VAL* 3.2 31.5 - - + +
127B ARG* 3.8 9.0 + - - -
148B ALA 3.9 3.3 + - - -
149B LEU* 4.2 4.0 - - + -
150B THR* 3.2 33.4 + - - +
151B PRO 3.3 4.3 - - - +
152B ARG* 1.3 76.1 - - - +
154B ARG* 1.3 68.0 + - - +
155B ALA 3.8 10.3 - - - +
184B HIS 5.4 0.3 - - - +
186B LEU* 2.9 33.7 - - + +
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Residues in contact with ARG 154 (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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2A ARG* 5.8 10.0 - - - +
98B LEU 4.2 7.0 - - - +
99B VAL* 3.8 16.4 - - + -
102B GLY 5.8 1.0 + - - -
103B ASP* 3.5 40.5 + - + +
104B GLU 2.8 11.9 + - - +
151B PRO 3.7 9.7 + - - -
152B ARG* 2.7 38.9 + - - +
153B THR* 1.3 80.3 + - - +
155B ALA* 1.3 61.5 + - + +
185B ASP 4.7 1.4 - - - +
186B LEU* 3.5 10.8 - - - -
187B PHE* 3.1 28.6 + - + +
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Residues in contact with ALA 155 (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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95B LEU* 6.2 0.2 - - + -
98B LEU* 4.6 11.2 - - + -
99B VAL* 5.0 2.2 - - + -
104B GLU 3.9 1.6 + - - -
105B VAL* 3.5 16.7 - - + +
106B VAL 3.0 22.9 + - - -
153B THR* 3.7 8.7 - - - +
154B ARG* 1.3 84.8 - - + +
156B LEU* 1.3 65.2 + - - +
186B LEU* 3.9 4.6 - - - +
187B PHE* 3.2 30.3 - - + +
189B ILE* 5.0 4.7 - - + -
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Residues in contact with LEU 156 (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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105B VAL* 5.1 0.9 - - - -
106B VAL* 3.7 29.4 - - + +
107B VAL* 5.4 0.4 - - - +
108B LEU* 5.3 8.5 - - + -
145B LEU* 4.1 22.4 - - + -
149B LEU* 6.3 0.7 - - + -
155B ALA* 1.3 76.1 - - - +
157B LEU* 1.3 90.3 + - - +
158B LEU* 4.1 15.7 - - + +
177B ILE* 3.5 33.2 - - + +
180B LEU* 5.4 3.4 - - + -
181B ALA* 5.9 0.4 - - + -
186B LEU* 4.7 12.5 - - + +
187B PHE 3.0 6.2 + - - +
188B LEU* 3.8 18.2 - - + -
189B ILE* 3.2 27.2 + - - +
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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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91B LEU* 5.0 4.9 - - + -
95B LEU* 4.0 37.9 - - + -
105B VAL* 4.7 2.9 - - + -
106B VAL 3.3 13.2 + - - +
107B VAL* 4.6 11.9 - - + +
108B LEU* 4.4 15.4 + - - +
115B TYR* 3.6 53.5 - - + +
156B LEU* 1.3 87.3 - - - +
158B LEU* 1.3 72.5 + - - +
159B ASN* 5.1 0.7 - - - +
189B ILE* 3.4 24.2 - - + +
191B ASP* 5.0 0.7 - - + -
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Residues in contact with LEU 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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108B LEU* 4.2 16.6 - - + -
156B LEU* 4.1 11.9 - - + +
157B LEU* 1.3 81.8 - - - +
159B ASN* 1.3 78.6 + - - +
160B THR* 3.6 23.8 - - + +
169B PHE* 3.0 48.7 - - + -
174B LEU* 4.9 4.7 - - + -
177B ILE* 4.0 20.4 - - + -
188B LEU* 6.2 1.5 - - + +
189B ILE 2.7 14.0 + - - +
190B SER* 4.4 5.2 - - - +
191B ASP* 3.2 19.9 + - - +
206B LEU* 4.6 20.0 - - + -
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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