Contacts of the strand formed by residues 152 - 159 (chain B) in PDB entry 1P7G
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 GLN 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118B PHE* 3.4 23.8 - - + -
146B TYR* 3.8 7.6 - - - -
147B GLU* 2.9 33.4 + - + +
150B GLU* 4.4 1.7 - - - +
151B GLU* 1.3 76.7 - - - +
153B LEU* 1.3 69.6 + - - +
154B LEU* 4.1 21.3 - - + +
15C THR* 3.5 14.0 - - - +
16C LYS* 2.7 52.8 + - + +
18C TYR* 3.1 25.8 + - - +
58C LEU* 4.3 3.9 - - - +
65C ARG* 5.5 0.7 + - - -
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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
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111B ILE* 4.1 5.6 - - + -
114B LEU* 3.7 39.0 - - + +
115B ILE* 3.7 20.4 - - + +
118B PHE* 3.5 24.0 - - + +
119B PHE* 4.0 21.3 - - + -
144B LEU* 4.0 10.5 - - + -
145B VAL 3.5 7.2 - - - +
146B TYR* 4.7 5.2 - - + -
152B GLN* 1.3 79.8 - - - +
154B LEU* 1.3 69.8 + - - +
172B LEU* 3.5 31.6 - - + -
210B LEU* 4.3 12.3 - - + -
65C ARG* 4.7 4.3 + - - -
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Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PHE* 5.0 1.6 - - - -
144B LEU* 3.4 3.7 - - - -
145B VAL* 2.8 47.5 + - + +
147B GLU* 3.7 20.4 - - + -
152B GLN* 4.1 21.1 - - + +
153B LEU* 1.3 83.7 - - - +
155B ILE* 1.3 68.1 + - - +
156B LEU* 4.9 3.6 - - + -
18C TYR* 4.2 4.9 - - - +
58C LEU* 4.1 14.6 - - + -
61C LEU* 5.4 0.4 - - + -
65C ARG* 4.9 11.0 - - - +
80C LEU* 4.0 24.7 - - + -
84C LEU* 3.5 31.2 - - + -
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Residues in contact with ILE 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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119B PHE* 3.8 19.4 - - + -
125B PHE* 3.6 15.9 - - + +
128B GLU* 3.9 19.2 + - + +
129B PHE* 3.5 47.8 - - + +
132B ALA* 3.9 28.0 - - + -
142B ALA* 5.4 0.2 - - + -
143B ILE 3.1 9.2 - - - +
144B LEU* 4.0 15.9 - - + -
154B LEU* 1.3 77.0 - - - +
156B LEU* 1.3 72.0 + - - +
65C ARG* 5.0 1.0 - - - +
77C LEU* 3.5 24.3 - - + +
80C LEU* 4.5 2.4 - - - +
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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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132B ALA* 5.1 0.4 - - - +
142B ALA* 3.5 4.5 - - - -
143B ILE* 2.8 51.9 + - + +
145B VAL* 4.0 22.0 - - + -
154B LEU* 4.9 5.2 - - + -
155B ILE* 1.3 84.7 - - - +
157B GLN* 1.3 65.1 + - - +
158B ILE* 4.8 0.2 - - + -
164B MSE 4.0 9.2 - - - +
166B ALA* 3.9 37.5 - - + +
77C LEU* 4.1 18.6 - - + +
80C LEU* 3.9 25.1 - - + -
81C SER* 4.7 11.7 - - - +
84C LEU* 5.5 2.0 - - + -
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Residues in contact with GLN 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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132B ALA* 2.9 33.9 - - + +
135B ASN* 3.3 18.0 - - - +
136B VAL* 4.1 13.8 - - + +
137B GLU 5.0 0.8 - - - +
141B TRP 3.6 4.3 - - - +
142B ALA* 4.8 0.2 - - - +
156B LEU* 1.3 74.7 - - - +
158B ILE* 1.3 65.1 + - - +
159B GLU* 5.0 2.2 + - + +
164B MSE 3.3 41.9 - - + +
74C ARG* 3.2 47.3 + - - +
77C LEU* 4.0 27.3 + - + +
78C ARG* 4.7 0.8 - - - +
81C SER* 5.6 0.2 - - - -
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Residues in contact with ILE 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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136B VAL* 4.0 5.6 - - - +
140B GLY* 3.0 3.5 - - - -
141B TRP* 2.8 44.8 + - + +
143B ILE* 3.7 35.0 - - + -
156B LEU* 4.8 1.3 - - + -
157B GLN* 1.3 81.5 - - - +
159B GLU* 1.3 64.0 + - - +
160B LYS 3.8 6.1 - - - +
161B HIS 3.7 32.1 - - - +
163B LEU 3.3 7.2 - - - +
164B MSE 3.8 2.2 - - - +
165B HIS* 3.3 51.1 - - + +
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Residues in contact with GLU 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B VAL* 5.0 4.5 - - + -
137B GLU* 3.8 18.3 + - - +
139B VAL 3.6 6.7 - - - +
157B GLN* 5.0 2.6 + - - +
158B ILE* 1.3 72.6 - - - +
160B LYS* 1.3 75.5 + - + +
162B ASN 3.6 0.2 + - - -
163B LEU* 3.1 49.7 + - + +
164B MSE 3.3 27.5 - - + +
74C ARG* 5.0 0.9 - - - -
78C ARG* 3.0 31.7 + - - -
163C LEU* 6.1 0.7 - - - +
160D LYS* 3.6 20.5 + - + -
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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