Contacts of the strand formed by residues 149 - 158 (chain A) in PDB entry 6H2V
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 ALA 149 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A LYS* 3.0 26.1 + - - +
120A PHE 3.5 5.2 - - - -
121A ASP 4.1 4.5 - - - +
123A VAL* 3.7 14.1 - - + +
145A ALA 2.8 19.6 + - - +
146A LEU 3.4 0.2 - - - +
148A MET* 1.3 73.6 - - - +
150A ARG* 1.3 58.7 + - - +
152A ALA 3.4 29.2 - - - +
153A VAL* 3.7 9.2 - - + -
209A PHE* 3.3 9.6 - - + -
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Residues in contact with ARG 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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54A VAL* 4.6 2.8 - - - +
118A LYS* 3.1 48.3 + - + +
119A SER* 3.3 21.6 + - - +
120A PHE* 2.8 21.0 + - - +
121A ASP* 2.8 40.3 + - - +
149A ALA* 1.3 74.3 - - - +
151A THR* 1.4 63.7 - - - +
209A PHE* 3.3 17.7 - - - +
45B MET* 4.4 6.1 - - - +
48B LYS* 3.5 44.8 - - - +
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Residues in contact with THR 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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49A ASP* 3.6 25.8 - - - +
121A ASP* 2.9 22.0 + - - +
150A ARG* 1.4 82.2 - - - +
152A ALA* 1.3 59.1 + - + +
206A ARG* 4.5 0.4 - - - +
208A SER* 3.7 5.4 - - - -
209A PHE* 3.4 18.2 - - - -
302A SO4 3.4 35.9 + - - +
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Residues in contact with ALA 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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49A ASP* 3.7 16.6 - - - +
121A ASP 3.3 3.2 + - - -
122A THR* 3.2 8.2 - - + +
123A VAL 3.0 23.0 + - - -
149A ALA* 3.4 5.7 - - - +
151A THR* 1.3 81.0 - - - +
153A VAL* 1.3 63.8 + - - +
154A TYR* 3.7 23.1 - - + -
206A ARG* 3.7 14.1 - - + +
207A PHE 3.3 11.9 - - - +
209A PHE* 4.3 2.6 - - - -
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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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123A VAL* 3.2 10.3 - - + +
125A MET* 4.0 15.3 - - + -
142A LEU* 4.1 12.6 - - + -
145A ALA* 3.6 48.9 - - + +
146A LEU* 3.8 16.6 - - + +
149A ALA* 3.7 9.4 - - + -
152A ALA* 1.3 75.5 - - - +
154A TYR* 1.3 65.9 + - - +
155A SER* 4.1 0.4 - - - -
205A ILE 3.6 1.0 - - - +
206A ARG* 3.5 4.0 - - - +
207A PHE* 2.9 44.5 + - + +
209A PHE* 5.0 1.3 - - + -
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Residues in contact with TYR 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 MET* 4.1 4.2 - - + +
43A ILE* 3.6 52.2 - - + +
47A TYR* 3.2 16.7 - + - +
49A ASP* 2.7 24.6 + - - +
122A THR* 3.6 26.2 - - + -
123A VAL 2.8 9.5 + - - +
124A ILE* 3.4 4.4 - - + -
125A MET* 3.0 26.0 + - - +
152A ALA* 3.7 11.2 - - + -
153A VAL* 1.3 72.7 - - - +
155A SER* 1.3 60.9 + - - +
179A ILE* 3.7 23.6 - - + -
204A LEU* 4.4 8.3 - - + -
205A ILE 3.3 5.2 - - - +
206A ARG* 2.8 38.0 + - + -
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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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125A MET* 3.4 34.6 - - - +
127A PRO* 3.8 5.0 - - - +
153A VAL* 4.5 1.1 - - - -
154A TYR* 1.3 75.8 - - - +
156A LEU* 1.3 65.2 + - - +
157A HIS* 2.9 35.6 + - - -
203A ASP 3.4 1.2 - - - +
204A LEU* 3.7 4.3 - - - +
205A ILE* 2.9 34.1 + - - +
207A PHE* 4.1 9.4 - - - -
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Residues in contact with LEU 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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31A THR* 4.8 1.3 - - + -
35A ILE* 4.5 13.7 - - + -
39A MET* 4.1 21.3 - - - -
125A MET 3.4 10.7 + - - +
126A ASN* 3.7 39.3 - - + +
127A PRO* 3.4 12.1 - - - +
129A PHE* 3.2 15.6 - - + -
155A SER* 1.3 75.3 + - - +
157A HIS* 1.3 64.2 + - - +
182A LEU* 3.7 27.1 - - + -
184A TYR* 4.3 8.3 - - - +
202A VAL* 3.8 22.0 - - + -
203A ASP 3.4 1.8 - - - -
204A LEU* 3.8 20.6 - - + -
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Residues in contact with HIS 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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129A PHE* 3.8 4.0 - - - -
138A ASP* 2.9 51.3 + - + +
139A MET* 4.3 3.9 - - - -
142A LEU* 3.8 23.0 - - + +
155A SER* 2.9 36.4 + - - -
156A LEU* 1.3 71.5 + - - +
158A LYS* 1.3 64.1 + - - +
161A THR* 5.2 0.9 - - - +
165A VAL* 4.0 21.3 - - + -
202A VAL* 3.6 4.9 - - - -
203A ASP* 2.8 33.4 + - - +
205A ILE* 3.8 24.0 - - + -
207A PHE* 3.8 8.6 - + - -
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Residues in contact with LYS 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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129A PHE* 3.8 38.2 - - + -
138A ASP* 4.9 1.2 + - - -
157A HIS* 1.3 76.2 - - - +
159A SER* 1.3 62.8 + - - +
160A SER* 3.9 16.8 - - - +
161A THR* 3.2 29.6 + - + +
162A ARG* 3.7 5.7 + - - -
194A LYS* 6.1 1.0 - - - +
199A ASP 5.2 4.6 + - - -
200A ILE* 4.0 28.6 - - + +
201A GLU 3.5 12.1 - - - +
202A VAL* 4.0 1.5 - - - +
203A ASP* 4.3 2.4 - - - +
15C GLN* 3.8 21.8 - - - +
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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