Contacts of the strand formed by residues 145 - 153 (chain B) in PDB entry 4JDA
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 ARG 145 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B PHE* 3.7 9.3 - - + -
121B GLU* 5.6 2.7 - - - +
131B SER* 5.8 1.3 - - - +
132B PHE 3.4 11.0 - - - +
133B ARG* 4.3 10.5 - - + -
143B ASN 3.5 2.9 + - - +
144B TYR* 1.3 77.9 - - - +
146B SER* 1.3 61.1 + - - +
172B TYR* 3.2 4.2 - - - +
173B ILE* 2.9 47.3 + - + +
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Residues in contact with SER 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 4.2 0.7 - - - -
131B SER* 2.6 27.6 + - - -
132B PHE* 3.0 32.2 + - - -
144B TYR* 3.6 27.2 + - - -
145B ARG* 1.3 75.9 - - - +
147B VAL* 1.3 63.2 + - - +
148B THR* 4.0 4.0 + - - -
170B GLU* 3.7 21.3 - - - +
171B SER 3.2 10.7 + - - -
172B TYR* 4.1 0.4 - - - +
301B A9S 5.7 0.2 - - - -
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B HIS* 3.5 29.4 - - + +
41B HIS* 3.0 19.4 - - + +
43B PHE* 4.0 18.2 - - + -
122B VAL* 6.1 0.2 - - + -
129B ILE* 4.0 15.7 - - + -
130B LEU 3.6 10.8 - - - +
131B SER* 3.4 14.4 - - - +
146B SER* 1.3 83.6 + - - +
148B THR* 1.3 63.8 + - - +
170B GLU* 3.3 0.2 - - - -
171B SER* 2.8 39.9 + - - +
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Residues in contact with THR 148 (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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41B HIS* 4.1 1.3 - - - -
69B VAL* 4.5 24.7 - - + -
78B TYR* 5.7 2.8 + - - +
129B ILE* 3.2 6.6 - - - +
130B LEU* 2.9 41.0 + - - +
132B PHE* 6.0 1.2 - - - -
146B SER* 4.0 3.3 + - - -
147B VAL* 1.3 74.4 - - - +
149B SER* 1.3 63.1 + - - +
168B VAL* 3.7 19.5 - - + -
169B LEU 3.1 14.4 - - - +
170B GLU* 2.9 33.2 - - - -
197B LEU* 5.1 1.6 - - + -
200B LEU* 6.0 0.4 - - + -
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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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36B ILE* 4.3 5.1 - - - +
41B HIS* 3.0 25.9 + - - -
127B LYS 5.2 0.9 - - - -
128B ARG 3.4 5.4 - - - -
129B ILE* 3.8 22.7 - - - -
148B THR* 1.3 77.9 - - - +
150B VAL* 1.3 63.0 + - - +
151B ASN* 3.0 22.0 + - - -
168B VAL* 3.4 4.7 - - - -
169B LEU* 2.9 30.3 + - - +
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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
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62B ALA* 3.5 36.5 - - + +
65B ILE* 3.9 35.4 - - + -
66B TRP* 4.4 16.4 - - + +
69B VAL* 4.0 18.2 - - + -
127B LYS 4.1 4.7 - - - +
128B ARG* 3.1 30.8 + - + +
148B THR* 5.7 0.2 - - + -
149B SER* 1.3 75.0 - - - +
151B ASN* 1.3 65.9 + - - +
152B GLU 4.2 1.1 + - - -
166B SER* 3.9 4.5 - - - -
167B VAL 3.8 2.5 - - - -
168B VAL* 4.3 10.1 - - + +
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Residues in contact with ASN 151 (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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33B LEU* 4.3 16.2 - - + +
36B ILE* 4.4 22.4 - - - +
127B LYS 5.2 3.6 - - - +
149B SER* 3.0 31.5 + - - -
150B VAL* 1.3 75.4 - - - +
152B GLU* 1.3 59.8 + - - +
153B PHE* 3.3 19.5 - - + -
166B SER* 3.2 3.2 - - - -
167B VAL 2.8 43.2 + - - +
169B LEU* 4.1 11.9 - - - +
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Residues in contact with GLU 152 (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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61B PRO* 3.3 15.1 - - - +
62B ALA* 2.9 39.5 + - + +
63B HIS* 4.7 0.7 + - - -
128B ARG* 5.2 5.7 + - - +
150B VAL 4.2 1.8 + - - -
151B ASN* 1.3 73.6 - - - +
153B PHE* 1.3 72.4 + - - +
154B VAL* 4.3 1.7 + - + +
164B VAL* 5.6 6.1 - - - -
165B TYR 3.6 14.4 - - - +
166B SER* 4.0 3.1 - - - +
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Residues in contact with PHE 153 (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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28B ASP 5.4 0.2 - - - -
29B GLU* 4.1 27.1 - - + -
32B THR* 4.2 20.2 - - + -
33B LEU* 3.8 22.0 - - + -
151B ASN* 3.3 36.1 - - + -
152B GLU* 1.3 79.2 - - - +
154B VAL* 1.3 61.3 + - - +
155B VAL* 3.9 0.8 + - + -
164B VAL* 3.9 3.5 - - - -
165B TYR* 2.6 67.9 + + + +
167B VAL* 3.8 27.8 - - + -
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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