Contacts of the strand formed by residues 126 - 135 (chain B) in PDB entry 3DRB
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 VAL 126 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B LEU* 3.8 21.3 - - + -
122B ASP 2.8 16.5 + - - +
123B PRO* 3.5 15.3 - - - +
125B TYR* 1.3 69.4 - - - +
127B LEU* 1.3 62.1 + - - +
128B SER 3.6 4.3 - - - +
243B GLY* 3.5 30.0 - - - +
244B GLY* 3.7 11.9 - - - -
295B VAL* 3.6 32.8 - - + -
296B HIS 3.6 2.7 - - - -
297B ILE* 3.4 19.1 - - + -
357B VAL* 4.0 13.7 - - + -
361B ILE* 4.7 1.8 - - + -
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Residues in contact with LEU 127 (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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123B PRO 5.1 1.3 - - - -
125B TYR 3.1 13.5 - - - +
126B VAL* 1.3 73.5 - - - +
128B SER* 1.3 63.6 + - - +
242B LYS* 3.4 14.0 - - + +
243B GLY 2.8 15.3 + - - -
296B HIS* 2.9 20.7 + - + +
297B ILE 4.4 0.2 - - - -
298B LYS* 3.0 44.4 - - + +
333B VAL* 4.0 27.1 - - + -
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Residues in contact with SER 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B VAL* 3.4 2.0 - - - -
127B LEU* 1.3 82.3 - - - +
129B SER* 1.3 59.2 + - - +
240B MET* 6.0 0.9 - - - -
241B GLN 3.3 14.1 - - - -
242B LYS* 4.0 12.8 - - - -
243B GLY 3.2 10.8 - - - -
295B VAL* 3.1 10.4 - - - +
296B HIS* 3.1 34.3 + - - +
400B ADP 2.7 35.9 + - - -
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Residues in contact with SER 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 4.4 0.9 - - - +
128B SER* 1.3 72.8 - - - +
130B ARG* 1.3 61.1 + - - +
240B MET* 3.2 4.5 - - - +
241B GLN* 2.9 32.2 + - - -
243B GLY 3.1 15.0 + - - -
244B GLY* 3.4 16.3 - - - -
245B ASN 4.6 1.1 - - - -
246B MET* 4.0 22.0 + - - +
249B VAL* 3.7 21.5 - - - +
294B GLY 3.6 4.5 - - - -
295B VAL* 3.5 11.1 - - - +
400B ADP 4.8 0.7 - - - -
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Residues in contact with ARG 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B SER* 1.3 75.3 - - - +
131B VAL* 1.3 69.6 + - - +
132B ARG* 3.5 20.3 - - - +
191B HIS 5.0 1.0 + - - -
228B TRP* 4.0 10.3 - - - -
238B ILE* 3.4 38.8 - - + +
239B SER 3.2 11.4 - - - +
240B MET* 3.8 19.8 - - + -
246B MET* 4.0 1.3 - - - +
249B VAL* 4.2 0.4 - - - -
292B ARG* 3.5 19.2 + - - +
293B ALA* 3.3 2.6 - - - -
294B GLY 2.9 34.0 + - - +
400B ADP 3.1 88.0 + - + +
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Residues in contact with VAL 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ARG* 1.3 81.2 - - - +
132B ARG* 1.3 63.5 + - - +
238B ILE* 3.6 0.7 - - - -
239B SER 2.7 34.1 + - - -
246B MET* 3.6 18.8 - - - -
249B VAL* 3.6 20.4 - - + -
250B PHE* 4.1 17.7 - - + -
253B PHE* 3.6 40.7 - - + -
291B LEU* 4.1 17.9 - - + -
292B ARG 3.7 3.4 - - - -
293B ALA* 4.0 9.6 - - + -
350B VAL* 4.9 0.2 - - + -
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Residues in contact with ARG 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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130B ARG* 3.5 25.6 - - - +
131B VAL* 1.3 76.0 - - - +
133B THR* 1.3 70.9 + - - +
134B GLY 4.9 0.6 - - - +
236B ARG* 3.9 15.6 - - + +
237B VAL 3.1 13.5 - - - +
238B ILE* 3.8 16.6 - - + -
253B PHE* 4.0 3.1 - - - -
281B LEU* 5.6 0.2 - - - +
286B ASN* 3.2 33.7 + - - +
290B GLY* 2.8 29.1 + - - -
291B LEU* 3.1 8.1 - - - +
292B ARG* 2.8 67.7 + - + +
320B ARG* 4.5 5.3 - - - +
341B ARG* 4.2 2.8 - - - +
400B ADP 2.3 33.1 + - - +
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Residues in contact with THR 133 (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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132B ARG* 1.3 79.4 - - - +
134B GLY* 1.3 67.2 + - - +
135B ARG* 2.9 21.1 + - - +
236B ARG* 3.3 11.8 - - - +
237B VAL* 2.8 39.7 + - + +
253B PHE* 3.3 28.5 - - + -
257B LEU* 4.1 9.2 - - + -
289B THR 2.6 26.9 + - - -
290B GLY 3.0 12.3 + - - -
291B LEU* 4.3 1.8 - - - -
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Residues in contact with GLY 134 (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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132B ARG* 4.9 0.4 - - - +
133B THR* 1.3 78.3 + - - +
135B ARG* 1.3 83.0 + - - -
235B LEU 3.1 12.1 - - - -
236B ARG* 3.8 10.7 - - - +
237B VAL 4.7 0.7 - - - -
279B TYR* 4.6 1.4 - - - +
281B LEU* 3.4 28.6 - - - +
290B GLY 3.8 4.4 + - - -
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Residues in contact with ARG 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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110B LEU* 4.8 2.8 - - - +
133B THR* 2.9 21.3 + - + +
134B GLY* 1.3 93.0 + - - +
136B SER* 1.3 63.6 + - - +
137B ILE* 5.5 0.2 - - - -
234B HIS* 3.5 6.1 + - - +
235B LEU* 2.9 42.4 + - + +
237B VAL* 5.1 4.5 - - + -
257B LEU* 3.3 43.7 - - + +
271B PHE* 3.5 46.8 - - + -
279B TYR* 3.3 58.7 + - - +
281B LEU* 3.4 5.1 - - - +
289B THR 3.8 3.0 + - - -
346B GLU* 4.5 8.1 + - - -
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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