Contacts of the strand formed by residues 139 - 148 (chain A) in PDB entry 2A1H
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 SER 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A LYS* 3.2 34.0 + - - +
80A ALA 3.4 14.1 - - - -
81A PHE* 3.9 20.9 - - - +
132A VAL* 5.2 0.4 - - - -
133A PRO* 3.6 19.6 - - - +
137A GLY 5.0 0.9 + - - -
138A THR* 1.3 79.4 - - - +
140A LEU* 1.3 61.2 + - - +
169A PRO* 3.6 0.7 - - - +
170A VAL* 2.9 33.6 + - - +
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Residues in contact with LEU 140 (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 THR* 3.9 20.0 - - + -
79A LYS* 3.4 3.3 - - - -
80A ALA* 2.9 44.9 + - + +
125A ILE* 3.9 20.2 - - + -
128A ASP 5.2 1.6 - - - +
131A TRP* 4.2 12.8 - - + +
132A VAL* 3.8 28.2 - - + +
133A PRO* 4.5 0.2 - - - +
139A SER* 1.3 77.2 - - - +
141A TYR* 1.3 66.2 + - - +
142A VAL* 3.7 2.2 + - + +
167A LEU* 3.9 24.0 - - + -
168A CYS 3.7 22.2 - - - +
169A PRO* 3.9 10.8 - - + -
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Residues in contact with TYR 141 (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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30A PHE* 3.7 30.3 - + - -
75A PHE* 5.1 0.7 - - - -
77A GLY* 3.4 28.5 - - - -
78A MET 3.6 8.7 - - - -
79A LYS* 4.3 13.9 - - + -
139A SER 4.1 1.6 + - - -
140A LEU* 1.3 71.9 - - - +
142A VAL* 1.3 61.7 + - - +
143A ARG* 2.9 47.6 + - + -
166A ILE 4.0 0.5 - - - +
167A LEU* 3.4 6.9 - - - +
168A CYS* 2.8 49.9 + - - +
170A VAL* 4.2 13.6 - - + +
202A LYS* 5.7 0.3 - - - -
313A THR* 4.1 14.4 - - + -
314A ALA 5.4 0.2 - - - -
502A GBN 3.5 18.0 - - - +
153B LEU* 3.9 21.1 - - + -
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Residues in contact with VAL 142 (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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77A GLY* 3.5 4.9 - - - -
78A MET* 2.8 51.2 + - + +
80A ALA* 4.6 1.6 - - + -
90A LEU* 4.0 12.8 - - + -
121A ILE* 3.9 19.5 - - + -
125A ILE* 3.9 24.0 - - + -
140A LEU* 4.1 9.6 - - + +
141A TYR* 1.3 77.9 - - - +
143A ARG* 1.3 62.2 + - - +
144A PRO* 3.4 10.5 - - + +
165A VAL* 3.8 21.8 - - + -
166A ILE 3.9 2.0 - - - -
167A LEU* 3.9 11.2 - - + -
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Residues in contact with ARG 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PHE* 3.5 19.8 - - - -
76A GLU 3.0 19.6 + - - -
141A TYR* 2.9 35.3 + - + -
142A VAL* 1.3 75.2 - - - +
144A PRO* 1.4 68.8 - - - +
145A VAL* 3.8 3.8 + - + +
164A PHE 3.8 0.5 - - - +
165A VAL* 3.5 3.0 - - - -
166A ILE* 2.9 41.0 + - + +
168A CYS* 6.1 0.2 - - - -
502A GBN 3.6 14.3 - - - +
69B HIS* 3.0 44.1 + - + -
70B TYR* 2.9 32.9 + - - -
153B LEU* 3.5 28.3 + - + +
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Residues in contact with PRO 144 (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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75A PHE* 3.3 4.0 - - - +
76A GLU* 3.0 44.4 + - + +
77A GLY 4.5 0.2 - - - +
78A MET* 5.0 4.0 - - + -
97A MET* 4.6 6.1 - - + -
100A MET* 3.8 26.7 - - + -
117A LEU* 5.2 0.9 - - + -
121A ILE* 3.9 25.4 - - + -
142A VAL* 3.4 16.2 - - + +
143A ARG* 1.4 84.8 - - - +
145A VAL* 1.3 61.2 + - - +
164A PHE 3.5 6.1 - - - +
165A VAL* 3.9 15.0 - - + -
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Residues in contact with VAL 145 (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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74A LEU 3.3 15.0 - - - +
75A PHE* 4.3 2.9 - - + +
100A MET* 4.1 4.2 - - - +
143A ARG* 3.9 11.4 - - + +
144A PRO* 1.3 80.8 - - - +
146A LEU* 1.3 64.2 + - - +
147A ILE* 3.8 23.1 - - + -
162A LEU 3.9 1.0 - - - +
163A LEU* 3.3 5.7 - - - +
164A PHE* 2.8 60.0 + - + +
68B LEU 4.2 11.7 - - - +
69B HIS* 3.5 33.4 - - + +
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Residues in contact with LEU 146 (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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48A TRP* 3.9 14.1 - - + -
73A GLN* 3.5 2.1 - - - -
74A LEU* 3.1 44.0 + - + +
100A MET* 4.0 10.0 - - + +
104A ALA* 3.8 28.9 - - + -
109A LEU* 3.9 16.9 - - + +
110A PRO* 3.9 15.3 - - + +
112A PHE* 4.0 15.7 - - + -
145A VAL* 1.3 74.7 - - - +
147A ILE* 1.3 66.2 + - - +
161A ALA* 4.4 9.2 - - + -
162A LEU 3.5 16.8 - - - +
163A LEU* 3.9 17.0 - - + -
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Residues in contact with ILE 147 (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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61A LEU* 4.2 14.4 - - + -
67A SER* 3.7 23.1 - - - +
72A LEU 3.3 6.1 - - - +
73A GLN* 3.8 20.0 - - + -
109A LEU* 4.0 5.4 - - - -
145A VAL* 3.8 17.5 - - + -
146A LEU* 1.3 79.6 - - - +
148A GLY* 1.3 63.9 + - - +
149A ASN* 4.9 2.2 - - - +
161A ALA* 3.3 6.9 - - - +
162A LEU* 2.9 68.3 + - + +
164A PHE* 4.4 10.5 - - + -
68B LEU* 4.2 20.0 - - + +
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Residues in contact with GLY 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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65A SER* 3.3 1.4 + - - -
66A SER* 3.6 16.2 - - - -
67A SER* 3.1 27.0 + - - -
72A LEU* 2.8 19.1 + - - -
109A LEU* 3.7 19.5 - - - +
147A ILE* 1.3 75.9 - - - +
149A ASN* 1.3 60.1 + - - +
158A PRO* 4.1 2.9 - - - -
160A ARG 3.9 4.3 - - - -
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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