Contacts of the strand formed by residues 135 - 145 (chain B) in PDB entry 4JZJ
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 THR 135 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A LYS* 4.7 9.0 - - - -
130B GLN* 3.1 38.4 + - - +
131B LEU* 3.2 17.0 - - - +
133B SER* 3.6 7.8 + - - +
134B GLY* 1.3 84.0 - - - +
136B ALA* 1.3 61.8 + - - +
186B THR* 6.4 1.3 - - - -
187B LEU 3.7 4.3 - - - +
188B SER* 4.2 2.7 - - - +
189B LYS 3.7 9.4 - - - +
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Residues in contact with ALA 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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126B PRO* 3.9 7.9 - - + -
130B GLN* 4.1 1.6 - - - -
131B LEU* 3.7 14.6 - - + -
135B THR* 1.3 71.8 - - - +
137B SER* 1.3 61.8 + - - +
138B VAL* 4.9 1.6 - - + -
185B LEU 3.9 0.6 - - - +
186B THR* 3.3 4.9 - - - +
187B LEU* 2.4 59.4 + - + +
188B SER 4.1 1.6 - - - +
192B TYR* 3.7 34.8 - - + -
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Residues in contact with SER 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 5.9 1.6 - - - +
148A LEU* 3.5 20.8 - - - +
150A LYS* 3.1 28.6 + - - -
124B PHE 4.5 0.2 - - - +
125B PRO 4.1 0.9 - - - -
126B PRO* 3.2 25.7 - - - +
130B GLN* 3.1 24.3 + - - -
136B ALA* 1.3 71.1 - - - +
138B VAL* 1.3 62.8 + - - +
139B VAL* 4.1 4.5 + - - +
184B THR* 4.2 5.8 - - - -
185B LEU 3.7 3.4 - - - -
186B THR* 3.1 10.5 - - - +
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ILE* 4.5 0.9 - - + -
124B PHE 3.5 15.9 - - - +
126B PRO* 3.8 19.1 - - + -
136B ALA* 4.9 2.7 - - + +
137B SER* 1.3 80.3 - - - +
139B VAL* 1.3 60.9 + - - +
154B TRP* 3.2 33.6 - - + -
184B THR* 4.6 0.4 - - - +
185B LEU* 2.9 45.5 + - + +
187B LEU* 5.3 3.4 - - + -
192B TYR* 4.4 13.0 - - + -
198B TYR* 4.9 6.5 - - + -
215B PHE* 3.7 21.8 - - + -
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Residues in contact with VAL 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU* 3.9 32.3 - - + -
148A LEU* 4.3 14.4 - - + -
186A SER* 5.2 3.4 - - - +
188A VAL* 5.7 2.2 - - + -
123B ILE* 3.6 0.7 - - - -
124B PHE* 3.0 53.4 + - + +
137B SER 4.8 3.1 - - - +
138B VAL* 1.3 78.1 - - - +
140B CYS* 1.3 66.8 + - - +
141B LEU* 5.0 2.9 - - + -
154B TRP* 3.9 3.4 - - - -
182B SER* 5.1 7.9 - - - -
183B SER 3.3 9.6 - - - +
184B THR* 3.8 23.3 - - + +
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Residues in contact with CYS 140 (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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121B VAL* 3.8 15.7 - - - -
122B PHE 3.4 4.7 - - - -
123B ILE* 4.5 1.6 - - - +
139B VAL* 1.3 77.3 - - - +
141B LEU* 1.3 65.9 + - - +
142B LEU* 3.9 12.8 - - - -
152B VAL* 4.4 3.4 - - + -
154B TRP* 3.3 19.8 - - + -
182B SER* 3.5 3.1 - - - -
183B SER* 3.0 36.9 + - - +
200B CYS* 2.0 46.7 - - + -
202B VAL* 4.4 1.1 - - - -
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Residues in contact with LEU 141 (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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144A ALA* 4.4 8.3 - - + -
173A PHE* 3.8 23.1 - - + -
188A VAL* 3.8 33.4 - - + -
190A THR* 5.8 1.1 - - + -
120B SER 3.4 2.3 - - - +
121B VAL* 3.2 8.1 - - - +
122B PHE* 2.8 55.6 + - + +
124B PHE* 4.2 17.5 - - + -
139B VAL* 5.0 2.9 - - + -
140B CYS* 1.3 77.2 - - - +
142B LEU* 1.3 73.7 + - - +
143B ASN* 4.3 13.7 - - + +
181B LEU 3.4 14.8 - - - +
182B SER* 5.0 1.6 - - - -
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Residues in contact with LEU 142 (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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119B PRO* 3.7 13.9 - - + -
120B SER 3.8 3.6 - - - -
121B VAL* 4.0 1.6 - - + +
140B CYS* 3.9 12.3 - - - -
141B LEU* 1.3 82.2 - - - +
143B ASN* 1.3 58.7 + - - +
145B PHE* 3.3 19.0 - - + -
150B ALA* 4.1 18.8 - - + -
152B VAL* 3.6 27.4 - - + -
180B SER* 3.4 1.9 - - - -
181B LEU* 2.8 51.4 + - + +
202B VAL* 3.4 47.8 - - + -
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Residues in contact with ASN 143 (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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169A GLY 5.2 1.4 + - - -
171A HIS* 3.1 17.0 - - - -
188A VAL* 5.0 1.8 - - - +
190A THR* 3.5 31.9 + - - +
118B ALA 4.4 0.2 - - - +
119B PRO* 3.4 2.8 - - - +
120B SER* 3.1 41.4 + - - +
122B PHE* 4.4 8.3 - - + -
141B LEU* 4.3 15.4 - - + +
142B LEU* 1.3 75.1 - - - +
144B ASN* 1.3 89.0 + - - +
145B PHE* 3.6 1.8 - - - -
180B SER* 2.9 19.6 + - - -
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Residues in contact with ASN 144 (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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171A HIS* 3.3 16.5 + - - -
117B ALA* 3.9 14.2 - - - +
118B ALA 4.0 5.0 - - - +
143B ASN* 1.3 97.8 + - - +
145B PHE* 1.3 58.7 + - - +
173B ASP* 6.1 0.2 - - - -
176B ASP* 2.9 25.6 + - - +
178B THR* 3.2 26.6 + - + +
179B TYR 3.3 2.8 + - - -
180B SER* 3.1 8.3 + - - -
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Residues in contact with PHE 145 (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 ALA* 3.3 15.0 - - - +
119B PRO* 3.5 31.6 - - + -
142B LEU* 3.3 35.0 - - + -
144B ASN* 1.3 75.3 - - - +
146B TYR* 1.3 62.6 + - - +
147B PRO 3.2 20.0 - - - -
148B ARG* 3.5 28.9 - - - -
150B ALA* 4.2 9.9 - - + -
169B VAL* 5.2 2.2 - - + -
178B THR* 3.6 2.1 - - - -
179B TYR* 3.0 47.4 + - + -
180B SER 4.4 1.6 - - - -
181B LEU* 3.5 30.5 - - + -
204B HIS* 3.8 9.2 - + - +
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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