Contacts of the strand formed by residues 148 - 156 (chain B) in PDB entry 3JRQ
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 LYS 148 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B TYR* 4.3 16.1 + - + -
56B ARG* 5.7 0.9 - - - +
124B ASP* 3.5 25.0 + - - +
125B LEU* 5.7 2.2 - - - +
134B GLY* 4.9 1.2 - - - -
135B PHE 3.5 4.7 - - - +
136B SER* 3.3 18.4 - - - +
146B ASN 3.3 3.3 + - - +
147B TYR* 1.3 78.1 - - - +
149B SER* 1.3 65.6 + - - +
150B VAL* 3.4 30.5 - - - +
173B TYR* 3.0 4.7 - - - +
174B VAL* 2.9 45.4 + - + +
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Residues in contact with SER 149 (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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50B TYR* 3.9 0.9 - - - -
134B GLY* 3.1 21.2 - - - -
135B PHE* 3.0 29.3 + - - +
147B TYR* 3.5 21.7 + - - -
148B LYS* 1.3 77.5 + - - +
150B VAL* 1.3 71.0 + - - +
151B THR* 4.6 0.9 + - - -
171B GLU* 2.9 26.9 + - - -
172B SER 3.1 12.6 + - - -
173B TYR* 4.0 0.7 - - - +
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Residues in contact with VAL 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PHE* 3.6 27.4 - - + +
48B HIS* 3.3 13.7 - - + +
50B TYR* 3.5 17.7 + - + +
125B LEU* 4.5 9.0 - - + -
132B VAL* 4.0 18.8 - - + -
133B THR 3.4 12.1 - - - +
134B GLY* 4.0 2.5 - - - -
148B LYS* 3.4 27.8 - - - +
149B SER* 1.3 73.1 + - - +
151B THR* 1.3 67.7 + - - +
171B GLU* 3.2 4.7 - - - +
172B SER 2.9 30.5 + - - +
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Residues in contact with THR 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TRP* 5.0 0.9 - - - -
76B VAL* 4.0 22.9 - - + -
85B TYR* 5.2 6.6 + - - +
131B ARG 4.1 0.2 - - - +
132B VAL* 3.5 2.1 - - - -
133B THR* 2.7 48.7 + - - +
134B GLY* 4.6 0.4 - - - -
135B PHE* 5.7 3.1 - - - -
149B SER* 4.6 1.4 + - - -
150B VAL* 1.3 76.7 + - - +
152B THR* 1.3 67.7 + - - +
153B VAL* 4.8 0.2 - - + -
169B VAL* 3.8 20.9 - - + -
170B LEU 3.3 11.0 - - - +
171B GLU* 3.8 23.0 + - + +
198B LEU* 5.6 1.3 - - + -
201B LEU* 5.9 0.2 - - + -
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Residues in contact with THR 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B PHE* 3.9 22.7 - - + -
48B HIS* 2.8 30.9 + - + +
130B ARG 5.7 1.1 - - - +
131B ARG 3.4 7.6 - - - -
132B VAL* 3.8 24.5 - - + -
150B VAL* 4.3 0.7 - - + -
151B THR* 1.3 77.5 - - - +
153B VAL* 1.3 66.0 + - - +
154B HIS* 2.6 32.9 + - + -
169B VAL* 3.4 4.9 - - - +
170B LEU* 2.9 34.4 + - - +
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Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PRO* 3.8 26.7 - - + +
72B VAL* 4.1 8.1 - - + -
73B TRP* 3.9 23.1 - - + +
76B VAL* 4.3 23.8 - - + -
130B ARG 4.6 2.9 - - - +
131B ARG* 3.0 34.5 + - + +
151B THR* 4.8 1.6 - - + -
152B THR* 1.3 79.4 - - - +
154B HIS* 1.3 63.2 + - - +
155B ARG 4.3 0.3 + - - -
167B THR* 3.4 25.8 - - + -
168B VAL 3.8 2.7 - - - -
169B VAL* 4.4 3.8 - - + +
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Residues in contact with HIS 154 (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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40B LEU* 3.7 24.3 - - + +
43B SER* 3.3 34.7 + - - -
47B PHE* 5.7 1.6 - + - -
69B PRO* 4.6 1.8 - - - -
130B ARG 6.1 0.9 - - - -
152B THR* 2.6 39.8 + - + -
153B VAL* 1.3 77.1 + - - +
155B ARG* 1.3 62.4 + - - +
156B PHE* 3.7 7.5 - - + -
167B THR* 3.2 9.5 - - - -
168B VAL 2.8 47.8 + - - +
170B LEU* 3.3 20.5 - - + +
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Residues in contact with ARG 155 (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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69B PRO* 3.6 20.8 - - + +
70B GLU* 5.8 0.4 + - - -
131B ARG* 4.8 10.0 - - - +
153B VAL 4.3 0.8 + - - -
154B HIS* 1.3 74.8 - - - +
156B PHE* 1.3 71.5 + - - +
157B GLU* 2.3 40.9 + - - +
165B ILE* 3.3 34.1 - - + +
166B TRP 3.8 0.4 - - - -
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Residues in contact with PHE 156 (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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36B GLU* 3.6 27.8 - - + -
39B GLN* 3.5 36.3 - - + -
40B LEU* 3.4 39.3 - - + -
154B HIS* 3.7 11.4 - - + -
155B ARG* 1.3 78.7 - - - +
157B GLU* 1.3 73.9 + - - +
165B ILE* 3.3 5.0 - - - +
166B TRP* 2.9 59.1 + + + +
168B VAL* 3.5 36.1 - - + -
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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