Contacts of the strand formed by residues 130 - 136 (chain B) in PDB entry 4SBV
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 130 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B VAL* 4.3 0.5 - - - +
129B GLY* 1.3 75.0 - - - +
131B ILE* 1.3 63.4 + - - +
132B HIS* 3.4 22.5 - - + +
158B THR* 3.5 11.2 - - + -
159B GLY 3.3 9.2 - - - +
161B VAL* 3.9 8.9 - - - +
227B ALA 3.7 0.9 - - - +
228B MET* 3.7 8.8 - - - +
229B GLU* 3.0 39.5 + - + +
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Residues in contact with ILE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LEU* 4.1 14.8 - - + -
119B TYR* 3.1 48.7 - - + -
130B ALA* 1.3 75.3 - - - +
132B HIS* 1.3 63.7 + - - +
133B MET* 4.2 23.1 - - + -
157B VAL 4.1 0.4 - - - -
158B THR* 2.5 37.8 - - - +
159B GLY 3.0 20.2 + - - +
160B PRO 5.2 1.8 - - - +
161B VAL* 5.1 2.7 - - + +
183B ILE* 4.2 22.4 - - + -
226B THR* 4.5 4.5 - - - +
227B ALA 3.6 3.6 - - - +
228B MET* 3.9 14.8 - - - -
242B LEU* 5.4 2.0 - - + -
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Residues in contact with HIS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ALA* 3.4 6.3 - - + +
131B ILE* 1.3 84.7 - - - +
133B MET* 1.3 65.1 + - - +
147B VAL* 3.4 21.6 - - + +
150B LEU* 4.2 6.7 - - + -
156B TYR* 2.8 36.9 + - + -
157B VAL 3.2 4.7 - - - -
158B THR* 3.2 22.0 + - + +
225B VAL 3.5 0.7 - - - +
226B THR* 3.3 3.1 - - - -
227B ALA* 2.8 52.5 + - + +
229B GLU* 2.6 32.8 + - + -
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Residues in contact with MET 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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117B TYR* 4.5 3.8 - - - +
118B THR* 5.8 0.4 - - - -
119B TYR* 5.8 1.6 - - - -
131B ILE* 4.2 24.0 - - + -
132B HIS* 1.3 81.9 - - - +
134B GLY* 1.3 57.8 - - - +
150B LEU* 3.9 4.3 - - - -
155B GLY 3.9 3.1 - - - +
156B TYR* 3.3 9.9 - - - -
157B VAL* 3.2 33.0 + - + +
183B ILE* 4.4 16.2 - - + +
184B THR* 4.1 12.6 - - - +
185B ILE* 3.1 37.9 - - + -
224B LEU* 3.8 13.2 - - + -
225B VAL 3.1 10.1 - - - +
226B THR* 4.3 7.0 - - - -
242B LEU* 4.0 29.2 - - - -
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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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133B MET* 1.3 75.3 - - - +
135B PHE* 1.3 62.3 + - - -
150B LEU* 4.1 6.5 - - - +
153B LEU* 4.2 14.1 - - - -
154B LYS 4.1 7.9 - - - -
156B TYR 4.5 4.0 - - - -
185B ILE* 4.2 4.9 - - - +
224B LEU* 3.4 6.5 - - - +
225B VAL* 2.6 40.4 + - - -
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Residues in contact with PHE 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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91B VAL* 4.7 7.4 - - + -
115B ILE 5.5 0.2 - - - -
117B TYR* 4.4 16.8 - + - -
134B GLY* 1.3 77.3 - - - -
136B GLN* 1.3 61.3 + - - +
137B TYR* 3.4 42.1 - + + +
153B LEU* 3.0 23.5 - - - +
154B LYS* 3.2 18.7 + - + +
155B GLY* 5.6 0.4 - - - -
185B ILE* 3.5 33.2 - - + -
186B ALA* 3.8 5.6 - - - -
187B LEU* 3.2 54.3 - - + -
188B ASP* 4.1 1.8 - - - -
222B ALA* 4.9 1.3 - - + -
223B ARG 3.5 4.3 - - - +
224B LEU* 3.9 25.6 - - + -
108C SER* 5.4 0.5 + - - -
253C PRO 5.2 1.0 - - - +
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Residues in contact with GLN 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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135B PHE* 1.3 72.7 - - - +
137B TYR* 1.3 63.9 + - - +
138B ASP 4.0 0.9 - - - +
139B MET* 4.6 1.6 - - - -
141B ASP* 4.6 4.0 - - + -
142B THR 3.1 14.7 + - - +
143B LEU* 2.8 34.0 - - - +
144B PRO* 3.1 27.1 - - - +
153B LEU* 3.3 22.6 - - + +
222B ALA* 3.3 6.4 - - - +
223B ARG* 2.7 64.7 + - + +
225B VAL* 4.0 6.5 - - + -
108C SER* 5.3 2.5 - - - -
254C ILE* 4.5 13.0 - - + +
258C LEU* 4.3 5.7 - - - +
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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