Contacts of the strand formed by residues 165 - 175 (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 TYR 165 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B GLU* 2.9 33.9 + - - +
57B ARG* 4.0 20.6 - - + -
58B VAL 3.5 12.1 - - - +
59B ASP* 3.7 13.7 - - + +
60B ALA 4.0 7.9 - - - +
61B PRO* 5.6 0.2 - - - +
152B GLU* 3.5 4.7 - - - +
153B PHE* 2.6 75.7 + + + +
155B VAL* 3.6 29.5 - - + +
164B VAL* 1.3 77.0 - - - +
166B SER* 1.3 67.5 + - - +
167B VAL* 4.3 0.9 - - + -
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Residues in contact with SER 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B ARG* 3.6 3.3 - - - -
58B VAL* 3.0 31.8 + - - +
60B ALA 2.6 24.6 + - - -
62B ALA* 3.2 12.3 + - - +
65B ILE* 3.2 22.6 - - - +
150B VAL* 3.9 13.9 - - - -
151B ASN 3.2 14.4 - - - -
152B GLU* 4.1 2.3 - - - -
153B PHE* 4.6 0.4 - - - -
165B TYR* 1.3 80.6 - - - +
167B VAL* 1.3 63.7 + - - +
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 4.7 10.1 - - + -
29B GLU* 4.2 14.1 - - + +
33B LEU* 5.4 4.7 - - + -
55B ALA* 4.5 9.4 - - + -
56B HIS 3.8 7.4 - - - +
57B ARG* 3.7 26.7 - - + +
149B SER 3.6 1.9 - - - +
151B ASN* 2.8 34.6 + - + +
153B PHE* 3.8 26.9 - - + -
165B TYR* 4.3 0.9 - - + -
166B SER* 1.3 74.3 - - - +
168B VAL* 1.3 66.5 + - - +
169B LEU* 3.9 26.2 - - + -
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Residues in contact with VAL 168 (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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54B ILE 3.7 0.9 - - - +
55B ALA* 3.4 3.3 - - - -
56B HIS* 3.0 37.8 + - + +
58B VAL* 4.2 17.3 - - + -
65B ILE* 4.2 23.3 - - + -
69B VAL* 5.5 0.2 - - + -
148B THR* 3.7 26.7 - - + -
149B SER 3.4 6.7 - - - +
150B VAL* 4.3 12.8 - - + -
167B VAL* 1.3 75.8 - - - +
169B LEU* 1.3 64.1 + - - +
197B LEU* 3.9 25.5 - - + +
200B LEU* 4.4 8.7 - - + -
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Residues in contact with LEU 169 (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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25B LEU* 4.8 7.0 - - + -
33B LEU* 5.2 9.6 - - + -
36B ILE* 5.8 1.1 - - + -
37B ILE* 5.0 9.9 - - + -
41B HIS* 3.3 29.5 - - + +
53B LEU* 4.0 17.0 - - + -
54B ILE 3.4 1.6 - - - -
55B ALA* 3.8 26.2 - - + -
148B THR* 3.1 6.8 - - - +
149B SER* 2.9 40.0 + - - +
151B ASN* 4.1 10.5 - - - +
167B VAL* 3.9 13.0 - - + -
168B VAL* 1.3 72.8 - - - +
170B GLU* 1.3 60.1 + - - +
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Residues in contact with GLU 170 (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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52B SER 4.3 0.3 - - - +
53B LEU* 4.0 1.1 - - - -
54B ILE* 2.7 42.3 + - - +
78B TYR* 5.6 5.4 + - - -
79B LYS* 5.6 1.2 - - - -
132B PHE* 6.2 0.9 - - - -
144B TYR* 5.5 0.9 - - - +
146B SER* 3.7 14.6 - - - +
147B VAL 3.3 2.5 - - - -
148B THR* 2.9 33.2 - - + +
168B VAL 4.0 0.2 + - - -
169B LEU* 1.3 74.2 - - - +
171B SER* 1.3 61.5 + - - +
172B TYR* 5.3 1.9 - - + -
193B VAL* 3.4 36.9 - - + +
196B ASN* 4.8 5.2 + - - +
197B LEU* 4.0 20.0 - - + +
301B A9S 4.1 15.9 - - - +
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Residues in contact with SER 171 (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* 2.8 48.8 + - - -
43B PHE* 3.4 6.9 - - - -
52B SER 3.2 12.6 - - - -
53B LEU* 3.6 15.3 - - - -
146B SER* 3.2 4.5 + - - -
147B VAL* 2.8 35.5 + - - +
170B GLU* 1.3 75.8 - - - +
172B TYR* 1.3 62.8 + - - +
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Residues in contact with TYR 172 (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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43B PHE* 3.3 8.0 - - - -
50B CYS* 3.8 22.9 - - - -
51B THR* 2.4 35.9 + - - -
52B SER* 3.0 36.5 + - - -
54B ILE* 5.4 3.4 - - + -
144B TYR* 3.5 32.5 - + + +
145B ARG 3.2 12.3 - - - +
146B SER* 4.3 0.9 - - - -
170B GLU* 5.3 2.2 - - + -
171B SER* 1.3 77.0 - - - +
173B ILE* 1.3 63.1 + - - +
174B VAL* 4.1 6.1 - - + -
186B ARG* 3.3 23.2 + - - +
189B VAL* 3.4 28.9 - - + +
190B ASP* 2.7 23.8 + - - -
193B VAL* 4.4 9.6 - - + -
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Residues in contact with ILE 173 (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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43B PHE* 3.6 38.8 - - + -
44B PRO* 3.9 23.1 - - + +
45B ARG* 5.6 0.9 - - - -
46B SER* 4.8 3.4 - - - +
49B THR* 4.0 27.8 - - + +
50B CYS 3.2 11.4 - - - +
51B THR* 4.4 6.3 - - + -
143B ASN 4.7 4.3 - - - +
144B TYR* 3.3 2.3 - - - -
145B ARG* 2.9 44.3 + - + +
172B TYR* 1.3 75.8 - - - +
174B VAL* 1.3 70.1 + - - +
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Residues in contact with VAL 174 (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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49B THR* 3.2 6.7 - - - -
50B CYS* 2.8 48.5 + - + +
141B LEU* 3.5 51.1 - - + +
142B ASN 3.8 1.3 - - - +
143B ASN 4.2 6.5 - - - -
144B TYR* 3.8 14.8 - - + -
172B TYR* 4.1 14.6 - - + -
173B ILE* 1.3 79.6 - - - +
175B ASP* 1.3 69.5 + - - +
185B THR* 4.2 16.8 - - + -
189B VAL* 4.8 1.3 - - + -
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Residues in contact with ASP 175 (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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48B ASN 3.7 7.4 - - - +
49B THR* 3.8 15.9 - - - +
140B ARG 4.6 3.8 - - - +
142B ASN* 3.2 28.6 + - + +
143B ASN* 2.7 33.2 + - - +
174B VAL* 1.3 85.2 - - - +
176B ILE* 1.3 71.0 + - - +
177B PRO* 3.1 10.3 - - + +
185B THR* 4.9 0.5 - - - +
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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