Contacts of the strand formed by residues 131 - 139 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B LEU* 5.5 1.8 - - + -
108B ILE* 3.9 20.9 - - + -
130B ASN* 1.3 80.8 - - - +
132B TYR* 1.4 62.9 + - - +
133B LEU* 4.0 19.5 - - + -
205B ALA* 3.1 4.9 - - + +
206B GLY* 3.1 8.1 - - - -
207B ILE* 2.8 66.2 + - + +
209B MET* 4.1 6.7 - - - -
235B ARG* 4.0 30.7 - - + +
238B LEU* 4.1 12.3 - - + -
239B ALA* 4.4 5.6 - - + -
242B LEU* 3.8 17.5 - - + -
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Residues in contact with TYR 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B THR* 3.8 7.4 - - + +
108B ILE* 3.3 23.4 - - - +
109B ALA 3.4 24.0 + - - +
110B GLU 3.4 23.6 - - - -
111B TYR* 4.1 0.9 - - - -
112B GLN* 3.7 29.4 - - + +
123B TRP* 4.2 10.5 - - - -
124B PHE 4.6 0.2 - - - -
125B SER* 3.1 24.6 - - - -
126B PRO* 2.8 36.4 + - - +
130B ASN* 3.7 35.5 + - + -
131B LEU* 1.4 75.9 - - - +
133B LEU* 1.3 64.6 + - - +
205B ALA 3.6 2.9 - - - -
501B BTN 3.5 21.3 - - + -
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B THR* 4.0 1.0 + - - -
106B ALA* 5.3 0.9 - - + -
107B CYS 3.4 10.3 - - - +
108B ILE* 3.8 15.7 - - + -
131B LEU* 4.0 19.7 - - + -
132B TYR* 1.3 77.3 - - - +
134B SER* 1.3 80.7 + - - +
135B MET* 4.7 2.5 - - + +
203B ILE* 5.0 2.2 - - + +
205B ALA* 2.8 45.3 + - + +
239B ALA* 4.4 1.3 - - - +
242B LEU* 4.4 12.1 - - + -
243B ILE* 3.0 42.2 - - + -
246B LEU* 4.8 17.0 - - + -
501B BTN 4.1 1.9 - - - +
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Residues in contact with SER 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B THR* 2.5 37.5 + - - -
91B ASN* 2.5 27.0 + - - -
94B LEU* 3.9 19.5 - - - +
106B ALA* 3.4 7.4 - - - +
107B CYS* 3.0 29.9 + - - +
133B LEU* 1.3 80.9 + - - +
135B MET* 1.4 58.7 + - - +
202B VAL* 4.8 0.4 - - - -
203B ILE 3.0 7.0 - - - -
204B GLY* 3.7 0.3 - - - -
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Residues in contact with MET 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LEU* 4.1 3.2 - - - +
104B GLY* 4.1 9.6 - - - +
105B ASP 3.6 11.2 - - - +
106B ALA* 4.6 3.6 - - + -
133B LEU* 4.7 2.4 - - + +
134B SER* 1.4 71.9 - - - +
136B PHE* 1.3 79.2 + - - +
137B TRP* 4.3 4.0 - - + -
201B ILE 3.5 0.3 - - - +
202B VAL* 3.4 3.1 - - - -
203B ILE* 2.6 56.6 + - + +
243B ILE* 3.6 48.7 - - + +
246B LEU* 3.9 28.9 - - + -
247B ARG* 3.6 19.1 - - + -
250B LEU* 4.0 16.4 - - - -
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Residues in contact with PHE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LEU* 4.2 8.1 - - + -
98B ILE* 3.3 46.2 - - + -
101B LEU* 3.6 31.2 - - + -
102B LYS 3.5 16.4 - - - +
103B SER* 3.9 14.6 - - - -
104B GLY* 2.7 33.3 + - - -
105B ASP* 2.9 16.6 + - + +
135B MET* 1.3 79.8 - - - +
137B TRP* 1.3 73.4 + - - +
138B ARG* 4.2 8.3 - - + -
200B GLN* 3.4 33.0 - - + -
201B ILE 3.2 10.1 - - - -
202B VAL* 4.1 5.8 - - + -
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Residues in contact with TRP 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B SER* 4.0 13.4 - - - +
104B GLY* 3.7 30.7 - - - -
135B MET* 3.9 2.9 + - - -
136B PHE* 1.3 81.0 - - - +
138B ARG* 1.3 74.0 + - - +
139B LEU* 3.3 22.7 - - + +
149B LEU* 6.0 1.8 - - + -
200B GLN* 3.5 2.1 - - - -
201B ILE* 2.5 50.9 + - + +
203B ILE* 3.9 18.4 - - + -
247B ARG* 3.3 27.6 - - + -
250B LEU* 3.0 52.5 + - + +
251B GLU* 3.5 20.4 - - + -
254B GLU* 3.6 27.7 + - - +
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Residues in contact with ARG 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ILE 5.4 2.2 + - - -
101B LEU 5.8 0.9 - - - -
102B LYS* 4.5 18.8 - - - +
103B SER* 3.0 19.6 + - - +
136B PHE* 4.2 12.8 - - + -
137B TRP* 1.3 78.2 - - - +
139B LEU* 1.3 71.9 + - - +
140B GLU* 3.5 22.9 + - - +
197B ASP* 4.0 11.7 + - - -
198B ALA* 3.5 27.4 + - + +
199B ALA 3.3 6.7 - - - +
200B GLN* 3.0 38.9 + - - +
254B GLU* 3.2 14.2 - - - +
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B TRP* 3.3 20.9 - - + +
138B ARG* 1.3 79.4 - - - +
140B GLU* 1.3 62.0 + - - +
141B GLN* 3.4 4.3 - - + +
142B GLY 3.4 9.5 + - - +
144B ALA 4.3 2.7 - - - +
145B ALA* 3.3 33.7 - - + -
149B LEU* 4.4 3.1 - - + -
198B ALA* 3.0 4.9 - - - -
199B ALA* 2.3 62.5 + - + +
201B ILE* 3.1 24.0 - - + -
253B PHE* 4.3 12.3 - - + -
254B GLU* 3.9 17.9 - - + +
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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