Contacts of the strand formed by residues 131 - 139 (chain A) in PDB entry 1HXD
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 131 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A LEU* 5.4 5.4 - - + -
108A ILE* 3.9 26.7 - - + -
130A ASN* 1.3 77.8 - - - +
132A TYR* 1.4 64.7 - - - +
133A LEU* 4.1 11.0 - - + -
205A ALA* 3.8 1.1 - - + +
206A GLY* 3.6 2.9 - - - -
207A ILE* 2.9 55.1 + - + -
209A MET* 3.9 14.3 - - - +
235A ARG* 4.5 8.1 - - + +
238A LEU* 3.6 11.9 - - + -
239A ALA* 4.3 19.1 - - + -
242A LEU* 3.0 34.3 - - + -
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Residues in contact with TYR 132 (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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90A THR* 4.0 5.0 - - + +
108A ILE* 3.2 29.4 - - - +
109A ALA 3.5 22.3 + - - +
110A GLU 3.1 26.7 - - - -
111A TYR* 4.0 5.6 - - - -
112A GLN* 3.9 24.0 - - + +
123A TRP* 4.5 11.4 - - - -
124A PHE 4.3 4.0 - - - -
125A SER* 3.4 32.1 - - - -
126A PRO* 2.7 35.1 + - - +
130A ASN* 3.0 43.2 + - + -
131A LEU* 1.4 75.0 - - - +
133A LEU* 1.3 58.8 + - - +
205A ALA 3.9 0.4 - - - -
207A ILE 6.0 0.2 - - - -
500A BTN 3.8 8.5 - - + -
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Residues in contact with LEU 133 (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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90A THR* 4.1 0.2 - - - -
106A ALA* 4.4 11.7 - - + -
107A CYS 3.5 9.9 - - - +
108A ILE* 3.9 17.0 - - + -
131A LEU* 4.5 9.2 - - + -
132A TYR* 1.3 75.1 - - - +
134A SER* 1.3 93.0 + - - +
135A MET* 5.4 4.9 - - + -
157A MET* 4.6 10.3 - - + -
203A ILE 5.6 0.4 - - - +
204A GLY* 3.1 1.0 - - - -
205A ALA* 2.8 45.7 + - + +
239A ALA* 5.3 1.3 - - - +
242A LEU* 3.8 37.7 - - + -
243A ILE* 4.5 13.0 - - + -
246A LEU* 5.1 6.1 - - + -
500A BTN 3.4 3.8 - - - +
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Residues in contact with SER 134 (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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90A THR* 2.4 50.3 + - - -
91A ASN* 2.8 24.3 + - - -
94A LEU* 3.7 11.7 - - - +
106A ALA* 3.3 8.0 - - - +
107A CYS* 3.1 31.0 + - - -
133A LEU* 1.3 78.0 + - - +
135A MET* 1.3 60.0 + - - +
202A VAL* 4.6 0.9 - - - -
203A ILE 2.8 6.3 - - - -
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Residues in contact with MET 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 4.2 4.0 - - - -
104A GLY* 3.6 24.0 - - - +
105A ASP 3.4 12.6 - - - +
106A ALA* 4.5 2.7 - - + -
133A LEU* 5.4 2.9 - - + -
134A SER* 1.3 74.1 - - - +
136A PHE* 1.3 63.9 + - - +
137A TRP* 4.5 0.4 - - - -
201A ILE 3.4 3.1 - - - +
203A ILE* 2.8 51.0 + - + +
243A ILE* 3.2 41.3 - - + -
246A LEU* 3.7 30.7 - - + -
247A ARG* 3.7 6.7 - - + -
250A LEU* 3.7 27.8 - - + -
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Residues in contact with PHE 136 (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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94A LEU* 4.0 5.2 - - + +
98A ILE* 3.0 44.2 - - + -
101A LEU* 3.7 31.2 - - + -
102A LYS 3.5 26.9 - - - -
103A SER 4.0 2.0 - - - -
104A GLY* 2.5 35.0 + - - -
105A ASP* 3.1 18.3 + - + +
135A MET* 1.3 71.6 - - - +
137A TRP* 1.3 78.0 + - - +
138A ARG* 4.1 22.2 - - + -
200A GLN* 3.8 16.4 - - + -
201A ILE 3.2 7.9 - - - -
202A VAL* 3.5 22.9 - - + -
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Residues in contact with TRP 137 (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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103A SER* 3.6 20.4 - - - -
104A GLY* 3.3 37.2 - - - -
136A PHE* 1.3 82.0 - - - +
138A ARG* 1.4 84.9 + - - +
139A LEU* 3.8 14.5 - - + +
149A LEU* 5.2 2.7 - - + -
200A GLN* 3.6 1.0 - - - -
201A ILE* 2.6 46.9 + - + +
203A ILE* 4.4 16.8 - - + -
247A ARG* 3.7 22.2 - - + -
250A LEU* 3.2 61.3 + - + -
251A GLU* 3.6 11.0 - - + -
254A GLU* 3.6 20.7 - - - -
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Residues in contact with ARG 138 (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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98A ILE* 4.7 7.1 + - - +
99A GLY* 5.4 4.2 - - - -
101A LEU 3.2 25.3 + - - -
102A LYS* 3.4 23.8 - - - +
103A SER* 2.9 16.2 + - - +
136A PHE* 4.1 16.5 - - + -
137A TRP* 1.4 83.2 + - - +
139A LEU* 1.3 57.0 + - - +
140A GLU* 4.3 2.6 + - - +
198A ALA* 3.4 28.0 - - + -
199A ALA 3.4 8.7 - - - +
200A GLN* 2.9 32.2 + - - +
254A GLU* 2.9 19.6 - - - +
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Residues in contact with LEU 139 (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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137A TRP* 3.8 18.4 - - + +
138A ARG* 1.3 78.5 - - - +
140A GLU* 1.3 64.0 + - - +
141A GLN* 3.7 13.5 - - - +
142A GLY 3.5 10.6 + - - +
143A PRO 6.1 0.4 - - - -
145A ALA* 3.3 33.4 - - + -
146A ALA* 4.2 8.1 - - + +
149A LEU* 5.1 3.8 - - + -
198A ALA* 2.8 30.5 - - - +
199A ALA* 2.9 16.1 + - + +
201A ILE* 3.8 22.0 - - + -
253A PHE* 5.0 12.3 - - + -
254A GLU* 3.9 21.3 - - + -
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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