Contacts of the strand formed by residues 152 - 159 (chain A) in PDB entry 3Q1H
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 TYR 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A HIS* 3.3 60.3 + + + +
26A PRO* 3.5 28.3 - - + +
114A THR* 4.1 6.5 - - + -
115A HIS 3.2 13.5 - - - +
116A ILE* 4.2 16.4 - - + -
140A GLU 4.6 2.9 - - - -
141A PHE* 3.4 9.3 - - - -
142A HIS* 2.9 61.0 + - + +
148A ASN* 3.7 8.3 + - - -
150A HIS 3.7 14.4 - - - +
151A SER* 1.3 76.0 - - - +
153A CYS* 1.3 63.3 + - - +
154A PHE* 3.9 18.2 - - + -
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Residues in contact with CYS 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LEU 3.5 0.2 - - - +
115A HIS* 2.8 58.9 + - + -
139A SER* 3.3 26.2 - - - -
140A GLU 3.4 16.6 - - - -
141A PHE* 4.2 15.0 - - + -
152A TYR* 1.3 78.3 - - - +
154A PHE* 1.3 62.4 + - - +
155A GLU* 5.1 1.1 - - - -
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Residues in contact with PHE 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TRP* 4.1 13.7 - + + -
24A HIS 3.6 14.1 - - - +
25A LEU* 3.6 20.4 - - + -
26A PRO* 3.7 33.0 - - + -
29A LEU* 3.7 21.1 - - + -
32A PHE* 6.5 0.2 - + - -
112A TYR* 3.9 35.2 - + + -
113A LEU 3.5 7.4 - - - -
114A THR* 3.4 24.9 - - - +
138A PHE* 3.9 3.7 - + - +
139A SER* 3.3 2.4 - - - -
140A GLU 2.9 34.1 + - - -
152A TYR* 3.9 4.6 - - + -
153A CYS* 1.3 71.7 - - - +
155A GLU* 1.3 59.7 + - - +
156A ILE* 3.7 23.6 - - + -
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Residues in contact with GLU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A MET 3.7 0.5 - - - +
112A TYR* 3.6 3.5 - - - -
113A LEU* 2.8 39.2 + - + +
115A HIS* 2.8 31.7 + - + +
129A TYR* 4.9 3.1 + - - -
136A SER* 2.7 34.1 + - - +
138A PHE 3.2 5.2 - - - +
139A SER* 4.3 10.0 + - - +
153A CYS* 5.1 0.9 - - - -
154A PHE* 1.3 77.0 - - - +
156A ILE* 1.3 66.1 + - - +
157A LEU* 3.4 29.7 + - + +
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Residues in contact with ILE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 4.2 12.3 - - + -
32A PHE* 6.1 3.6 - - + -
110A ARG* 4.2 19.1 - - + +
111A MET 3.3 8.7 - - - +
112A TYR* 4.0 16.2 - - + -
136A SER* 3.7 2.1 - - - -
137A VAL* 2.9 42.7 + - + +
138A PHE* 2.8 30.1 + - + +
154A PHE* 3.7 28.7 - - + -
155A GLU* 1.3 72.1 - - - +
157A LEU* 1.3 68.6 + - - +
158A GLU* 4.6 2.9 - - + -
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ARG* 3.2 6.9 - - - +
111A MET* 2.9 42.1 + - + +
113A LEU* 3.5 37.2 - - + -
129A TYR* 4.8 11.4 - - + +
134A TRP* 3.8 26.0 - - + -
135A GLU 3.1 8.3 - - - +
136A SER* 3.4 23.6 - - - +
155A GLU* 3.4 38.6 - - + +
156A ILE* 1.3 73.2 - - - +
158A GLU* 1.3 66.3 + - - +
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Residues in contact with GLU 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ILE* 5.2 0.7 - - - +
109A ASN* 3.6 9.6 - - - +
110A ARG* 2.8 45.9 + - + +
134A TRP* 3.6 5.7 - - - -
135A GLU* 2.8 33.5 + - + +
137A VAL* 4.3 27.2 - - + +
156A ILE* 4.6 2.2 - - + -
157A LEU* 1.3 79.3 - - - +
159A ARG* 1.3 67.7 + - - +
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Residues in contact with ARG 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A LEU* 2.9 32.1 + - - +
106A ASP* 3.8 16.1 + - - +
108A ALA 2.7 20.7 + - - -
109A ASN* 3.2 21.3 + - + +
133A GLU* 2.9 46.5 + - - +
134A TRP* 3.5 31.9 - - + +
135A GLU* 5.6 0.3 - - - +
158A GLU* 1.3 78.9 - - - +
160A ARG* 1.3 62.5 + - - +
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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