Contacts of the strand formed by residues 149 - 159 (chain A) in PDB entry 1A34
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 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A GLU* 4.3 13.1 - - + +
45A VAL 3.3 16.4 - - - +
46A SER* 4.1 13.6 + - - +
47A VAL 4.6 0.2 - - - +
82A THR* 3.9 1.7 - - - -
83A GLN* 2.9 45.8 + - + +
84A LEU* 3.9 36.1 + - + +
147A CYS* 3.3 5.5 - - - +
148A ARG* 1.3 80.8 - - - +
150A VAL* 1.3 65.7 + - - +
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Residues in contact with VAL 150 (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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44A GLU* 3.3 3.3 - - - +
45A VAL* 3.0 39.4 + - + +
47A VAL* 4.1 7.2 - - + +
80A ALA* 3.9 24.5 - - + -
81A TRP 3.4 13.5 - - - +
82A THR* 4.6 2.5 - - - -
83A GLN* 4.1 2.9 - - - -
94A VAL* 4.2 7.4 - - + -
143A VAL* 3.8 26.0 - - + -
145A SER* 3.8 30.3 - - - +
147A CYS 4.8 0.2 - - - +
149A GLN* 1.3 78.8 - - - +
151A ALA* 1.3 64.1 + - - +
152A LEU* 4.0 8.1 + - + +
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Residues in contact with ALA 151 (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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43A PHE 3.7 4.7 - - - -
44A GLU* 3.9 15.7 - - + +
80A ALA* 3.3 2.9 - - - -
81A TRP* 2.7 53.7 + - + +
83A GLN* 3.7 25.0 - - + +
119A ARG* 4.4 5.8 - - - +
150A VAL* 1.3 72.5 - - - +
152A LEU* 1.3 61.3 + - - +
153A VAL* 6.2 0.7 - - + -
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Residues in contact with LEU 152 (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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41A ILE 3.6 0.6 - - - +
42A PRO* 3.3 4.5 - - - +
43A PHE* 2.8 60.3 + - + +
45A VAL* 4.0 36.8 - - + -
55A VAL* 4.3 8.1 - - + -
78A VAL* 3.8 27.6 - - + -
79A ARG 3.3 7.2 - - - +
80A ALA* 4.0 13.2 - - + -
96A LEU* 4.6 0.2 - - + -
141A CYS* 4.6 6.7 - - - -
143A VAL* 4.6 13.0 - - + -
150A VAL* 4.4 3.8 - - + +
151A ALA* 1.3 79.5 - - - +
153A VAL* 1.3 64.7 + - - +
154A ILE* 4.1 8.3 - - + -
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Residues in contact with VAL 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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40A ALA* 4.1 22.0 - - + -
41A ILE 3.3 7.6 - - - +
42A PRO* 4.3 13.9 - - + -
77A SER 4.3 0.5 - - - +
78A VAL 4.0 0.3 - - - -
79A ARG* 2.9 57.1 + - - +
81A TRP* 3.7 26.9 - - + -
151A ALA* 5.6 1.8 - - + -
152A LEU* 1.3 79.7 - - - +
154A ILE* 1.3 63.1 + - - +
155A SER* 4.1 1.4 + - - +
8C U 4.7 0.2 - - - +
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Residues in contact with ILE 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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39A ARG 3.6 1.6 - - - +
40A ALA* 3.4 1.8 - - - -
41A ILE 2.9 38.6 + - - +
43A PHE* 3.7 31.4 - - + -
55A VAL* 5.1 1.6 - - + -
60A LEU* 4.3 15.0 - - + -
75A VAL* 3.8 24.9 - - + -
77A SER 3.6 9.0 - - - +
78A VAL* 4.2 17.5 - - + -
140A VAL* 4.5 26.5 - - + -
152A LEU* 4.5 8.3 - - + -
153A VAL* 1.3 78.2 - - - +
155A SER* 1.3 67.4 + - - +
156A CYS* 3.7 14.2 + - + -
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Residues in contact with SER 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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39A ARG 3.3 5.8 - - - -
40A ALA* 4.3 1.5 - - - +
75A VAL* 3.9 0.5 - - - -
76A MET* 2.9 33.5 + - - -
77A SER* 3.0 30.3 + - - +
79A ARG* 4.5 5.0 + - - -
153A VAL 4.1 1.1 + - - -
154A ILE* 1.3 70.3 - - - +
156A CYS* 1.3 63.1 + - - +
7C U 3.8 17.2 + - - -
8C U 3.4 31.4 + - - -
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Residues in contact with CYS 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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37A TRP 3.9 0.3 - - - +
38A VAL* 3.5 5.2 - - - +
39A ARG* 2.8 35.0 + - - +
41A ILE* 4.1 7.6 - - - -
60A LEU* 4.7 4.0 - - - -
73A VAL* 3.5 14.1 - - + -
74A THR 3.3 14.1 - - - +
75A VAL* 4.0 7.4 - - + -
76A MET* 3.8 5.6 - - - +
154A ILE* 3.9 20.9 - - + -
155A SER* 1.3 77.4 - - - +
157A CYS* 1.3 64.8 + - - +
158A PHE* 3.5 31.4 - - - -
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Residues in contact with CYS 157 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A THR* 6.2 1.6 - - - -
37A TRP 3.6 6.1 - - - +
38A VAL* 4.2 17.5 - - + +
73A VAL* 3.9 2.0 - - - -
74A THR* 2.8 45.3 + - - +
76A MET* 3.6 34.8 - - - -
156A CYS* 1.3 73.2 - - - +
158A PHE* 1.3 64.3 + - - +
159A ASN* 3.4 7.4 + - + +
4B A 6.0 1.8 - - - -
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Residues in contact with PHE 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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36A THR* 3.3 7.6 - - - -
37A TRP* 2.9 31.0 + - + +
39A ARG* 3.8 20.9 - - + -
41A ILE* 3.8 19.5 - - + -
60A LEU* 3.5 32.8 - - + -
61A PHE* 3.8 28.9 - + - -
67A THR* 3.7 18.8 - - + -
70A PHE* 3.6 37.5 - + + -
72A SER 4.0 2.0 - - - -
73A VAL* 3.9 10.1 - - + -
156A CYS* 3.5 27.6 - - - -
157A CYS* 1.3 73.9 - - - +
159A ASN* 1.3 60.1 + - - +
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Residues in contact with ASN 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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34A THR 5.8 0.3 - - - +
35A PRO 5.9 0.6 - - - -
36A THR* 3.7 22.7 - - + +
70A PHE* 3.6 19.0 - - - +
71A THR* 4.5 2.6 + - - -
72A SER* 3.2 30.1 + - - +
73A VAL* 4.1 2.6 - - - +
74A THR* 3.7 6.9 + - - +
133A ASN* 2.9 42.6 + - - -
157A CYS* 3.4 16.6 + - + +
158A PHE* 1.3 74.9 - - - +
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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