Contacts of the strand formed by residues 147 - 157 (chain A) in PDB entry 5V35
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 LEU 147 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A THR* 4.4 2.7 - - + -
40A MET 3.4 13.0 - - - +
41A LYS* 4.3 4.9 - - + -
42A CYS* 4.2 3.8 - - - -
49A ILE* 4.1 22.9 - - + -
87A PHE 3.6 1.4 - - - +
89A CYS* 2.9 36.0 + - - +
94A THR* 3.8 25.0 - - + +
97A TYR* 3.9 25.4 - - + -
140A LEU* 4.2 18.4 - - + -
145A GLN* 4.5 1.1 - - + +
146A PRO* 1.3 84.7 - - - +
148A VAL* 1.3 62.6 + - - +
149A PHE* 3.6 33.2 + - + -
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Residues in contact with VAL 148 (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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38A ARG 3.8 0.7 - - - +
39A THR* 3.6 1.0 - - - -
40A MET* 2.7 56.2 + - + +
41A LYS 4.2 6.5 - - - +
42A CYS* 3.4 26.2 - - + -
46A ARG* 4.0 15.9 - - - +
86A GLU* 3.2 42.0 - - + +
87A PHE 3.5 10.8 - - - +
88A TRP* 4.2 10.1 - - + +
147A LEU* 1.3 73.2 - - - +
149A PHE* 1.3 63.8 + - - +
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Residues in contact with PHE 149 (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 PHE* 5.7 0.2 - - + -
38A ARG 3.4 3.6 - - - +
39A THR* 3.0 40.8 - - + -
71A PHE* 5.3 4.9 - + - -
75A LEU* 4.6 7.6 - - + -
85A ALA 4.0 0.5 - - - +
86A GLU* 3.5 2.1 - - - -
87A PHE* 2.8 36.6 + - + +
89A CYS* 3.8 32.8 - - + -
93A HIS 6.0 1.6 - - - -
94A THR* 5.3 2.9 - - + -
97A TYR* 3.7 20.6 - + + -
147A LEU* 3.6 33.2 - - + -
148A VAL* 1.3 75.2 - - - +
150A VAL* 1.3 58.6 + - - +
151A ILE* 4.2 21.1 - - + -
201A FAR 3.5 20.9 - - + -
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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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17A LEU* 4.6 8.5 - - + -
36A HIS 4.5 0.2 - - - -
37A PHE* 3.2 4.3 - - - -
38A ARG* 2.8 62.7 + - - +
40A MET* 3.8 20.0 - - + -
46A ARG* 5.2 1.1 - - - +
84A VAL* 4.1 19.7 - - + -
85A ALA 3.4 7.2 - - - +
86A GLU* 3.8 31.4 - - + +
148A VAL 4.1 0.4 + - - -
149A PHE* 1.3 70.1 - - - +
151A ILE* 1.3 63.8 + - - +
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Residues in contact with ILE 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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35A PHE* 3.9 8.7 - - + -
36A HIS 3.1 10.1 - - - +
37A PHE* 4.1 12.3 - - + -
75A LEU* 4.6 12.1 - - + -
76A LEU* 3.8 31.0 - - + -
79A MET* 3.6 13.1 - - - +
84A VAL* 3.2 5.7 - - - +
85A ALA 2.8 34.3 + - - +
87A PHE* 3.7 29.2 - - + -
149A PHE* 4.2 16.8 - - + -
150A VAL* 1.3 81.6 - - - +
152A GLU* 1.3 66.0 + - - +
153A LEU 4.7 0.2 - - - +
201A FAR 4.9 11.4 - - + -
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Residues in contact with GLU 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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18A HIS* 5.7 1.4 - - - -
35A PHE* 3.2 7.0 - - - +
36A HIS* 2.9 35.3 + - + +
53A ARG* 2.6 34.8 + - - +
82A HIS* 4.5 15.8 - - - +
83A GLU 3.2 12.3 - - - +
84A VAL* 4.0 22.2 - - + +
151A ILE* 1.3 72.8 - - - +
153A LEU* 1.3 66.8 + - - +
154A LEU* 3.5 22.6 + - + +
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Residues in contact with LEU 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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25A PRO* 5.1 0.2 - - + -
27A PHE* 3.9 13.7 - - + -
33A VAL* 3.3 33.0 - - + -
34A ILE 3.6 13.7 - - - +
35A PHE* 4.1 5.4 - - + -
76A LEU* 4.3 4.3 - - + +
79A MET* 3.3 47.8 - - + +
80A ARG 3.6 19.5 - - - +
81A VAL* 4.2 7.4 - - + +
82A HIS* 2.9 28.9 + - - -
83A GLU 3.0 7.1 + - - -
151A ILE* 5.5 0.2 - - + -
152A GLU* 1.3 75.0 - - - +
154A LEU* 1.3 59.1 + - - +
155A GLN 4.0 6.7 - - - +
156A VAL* 4.0 10.5 - - + -
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Residues in contact with LEU 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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34A ILE* 2.8 31.7 + - + +
35A PHE* 4.0 8.3 - - - -
36A HIS* 4.2 16.8 - - + -
53A ARG* 5.0 0.9 - - - +
58A PRO* 3.6 34.3 - - + -
81A VAL* 3.8 16.5 - - - +
82A HIS* 4.2 14.1 + - + -
152A GLU* 3.8 31.4 - - + +
153A LEU* 1.3 73.3 - - - +
155A GLN* 1.3 62.5 + - + +
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Residues in contact with GLN 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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32A ARG 4.1 0.6 - - - +
33A VAL* 3.8 0.2 - - - -
34A ILE* 2.9 51.4 + - + +
81A VAL* 4.8 5.4 - - - -
153A LEU* 3.9 1.7 - - - +
154A LEU* 1.3 84.7 - - + +
156A VAL* 1.3 67.8 + - - +
157A ASP* 2.5 42.9 + - - +
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Residues in contact with VAL 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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25A PRO* 3.8 29.2 - - + -
26A ASN 4.1 15.7 - - - +
27A PHE* 3.9 30.1 - - + -
31A SER* 4.3 11.7 - - - -
32A ARG 3.6 8.7 - - - +
33A VAL* 4.5 4.9 - - + -
81A VAL* 4.2 12.6 - - + +
153A LEU* 4.0 13.5 - - + -
155A GLN* 1.3 79.7 - - - +
157A ASP* 1.3 70.2 + - - +
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Residues in contact with ASP 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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26A ASN 6.0 0.2 - - - -
31A SER* 3.1 7.8 - - - -
32A ARG* 2.9 40.8 + - + +
34A ILE* 3.7 11.1 - - - +
155A GLN* 2.5 42.0 + - - +
156A VAL* 1.3 82.8 - - - +
158A ALA* 1.3 64.4 + - - +
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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