Contacts of the strand formed by residues 152 - 159 (chain B) in PDB entry 1IVV
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 ILE 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139B ALA* 3.5 21.9 + - + +
147B GLU* 3.8 41.1 - - + +
150B ARG* 4.1 14.1 - - + +
151B ARG* 1.3 75.6 - - - +
153B LEU* 1.3 79.2 + - - +
154B ARG* 4.2 5.8 - - - +
178B TYR* 4.3 1.6 - - + -
179B VAL 3.2 22.7 - - - +
180B ASP* 3.9 18.8 - - + +
187B THR* 4.2 15.5 - - + +
559B ASN* 4.9 2.3 + - - +
560B GLN* 2.9 32.4 + - - +
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Residues in contact with LEU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B VAL* 4.0 32.1 - - + -
104B GLU* 3.6 27.6 - - + +
105B PHE* 4.0 24.5 - - + -
108B VAL* 3.8 20.8 - - + +
136B PRO* 4.2 1.3 - - + -
137B LEU 3.4 22.9 - - - +
138B SER* 4.1 2.9 - - - -
139B ALA* 4.6 0.9 - - - -
152B ILE* 1.3 82.2 - - - +
154B ARG* 1.3 64.4 + - - +
177B ALA 4.1 0.2 - - - +
179B VAL* 2.9 30.9 + - - +
181B VAL* 3.7 17.2 - - + +
559B ASN* 5.9 0.2 - - - +
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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
----------------------------------------------------------
108B VAL* 5.1 0.7 - - - -
135B ALA 3.4 1.2 - - - +
136B PRO* 3.7 1.4 - - - +
137B LEU* 2.8 34.9 + - - +
139B ALA* 3.1 42.7 + - + +
140B GLY 4.1 2.2 + - - -
142B PHE* 4.0 11.0 - - - +
144B TYR* 3.9 13.4 - - - -
147B GLU* 2.8 43.4 + - - -
152B ILE* 4.2 1.8 - - + +
153B LEU* 1.3 76.6 - - - +
155B GLY* 1.3 60.7 + - - +
176B VAL* 4.4 0.7 - - + -
177B ALA 3.3 8.1 - - - +
178B TYR* 3.3 38.8 - - + +
293B TRP* 3.4 50.6 - - + +
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Residues in contact with GLY 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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108B VAL* 4.4 7.0 - - - +
112B LEU* 4.9 1.8 - - - -
118B TRP* 4.4 5.7 - - - -
134B VAL* 3.6 18.2 - - - -
135B ALA 3.4 6.7 - - - -
153B LEU 4.2 0.2 + - - -
154B ARG* 1.3 75.8 - - - +
156B LEU* 1.3 63.0 + - - -
176B VAL* 3.3 10.8 - - - +
177B ALA 2.7 36.4 + - - -
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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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118B TRP* 5.0 0.2 - - - -
134B VAL* 3.4 5.0 - - - +
135B ALA 2.9 33.1 + - - +
137B LEU* 4.0 5.2 - - + -
155B GLY* 1.3 78.3 - - - +
157B ALA* 1.3 62.0 + - - +
158B PHE* 3.6 16.7 - - + -
172B VAL 5.7 1.1 - - - +
175B LEU 3.4 22.2 - - - +
176B VAL* 3.9 4.0 - - + -
290B ILE* 3.6 26.0 - - + +
291B ARG* 4.0 11.9 - - + +
293B TRP* 3.5 28.7 - - + -
294B GLN* 4.5 0.4 - - - +
407B PHE* 3.7 29.8 - - + -
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Residues in contact with ALA 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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118B TRP* 4.0 21.5 - - + -
122B LEU* 5.1 0.4 - - + -
132B VAL* 3.5 23.3 - - + -
133B ARG 3.5 4.5 - - - +
134B VAL* 4.6 0.7 - - - +
156B LEU* 1.3 72.3 - - - +
158B PHE* 1.3 71.1 + - - +
171B PRO* 3.8 0.7 - - - +
172B VAL* 2.9 48.3 + - + +
175B LEU* 4.6 7.4 + - + -
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Residues in contact with PHE 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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359A TRP* 4.2 19.5 - + + -
132B VAL* 3.7 1.8 - - - -
133B ARG* 2.8 35.6 + - - +
135B ALA* 4.0 6.3 - - + -
156B LEU* 3.6 20.9 - - + -
157B ALA* 1.3 78.0 - - - +
159B VAL* 1.3 63.0 + - - +
167B ALA* 3.5 33.2 - - + +
168B TRP* 3.8 16.8 - + - -
170B HIS 3.3 5.8 - - - -
171B PRO* 3.6 20.4 - - + -
172B VAL* 4.2 0.9 - - - -
407B PHE* 3.4 45.3 - + - -
408B THR* 3.4 24.9 - - - -
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Residues in contact with VAL 159 (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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127B LEU* 3.9 28.7 - - + -
131B LYS* 3.6 18.4 - - + +
132B VAL* 4.6 7.9 - - + +
158B PHE* 1.3 71.2 - - - +
160B GLN* 1.3 65.7 + - - +
161B ASP* 3.3 23.8 - - - +
167B ALA* 3.3 10.5 - - - -
170B HIS* 2.8 43.8 + - + +
172B VAL* 3.7 22.4 - - + -
197B VAL* 4.2 7.6 - - + -
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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