Contacts of the strand formed by residues 180 - 189 (chain B) in PDB entry 1JZ3
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 GLY 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128B ASN* 3.0 19.3 + - - -
129B VAL 2.8 37.8 + - - -
179B ALA* 1.3 74.7 - - - +
181B GLU* 1.3 61.8 + - - -
182B ASN* 2.9 8.3 + - - -
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Residues in contact with GLU 181 (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 THR* 3.3 29.2 - - + +
127B PHE* 3.8 11.6 - - - -
128B ASN* 3.3 31.4 + - - +
178B ARG* 3.0 28.0 + - - +
179B ALA 4.1 0.8 + - - -
180B GLY* 1.3 72.2 - - - -
182B ASN* 1.3 63.4 + - - +
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Residues in contact with ASN 182 (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 THR* 3.1 6.4 - - - +
127B PHE* 2.6 57.3 + - + +
129B VAL* 3.6 14.3 - - - +
155B ASN* 2.7 30.6 + - - +
177B LEU* 3.4 11.9 - - + +
178B ARG* 2.8 39.8 + - - +
180B GLY 2.9 21.8 + - - -
181B GLU* 1.3 76.2 - - - +
183B ARG* 1.3 62.7 - - - +
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Residues in contact with ARG 183 (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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73B TRP* 2.8 43.0 + - - +
74B LEU 3.2 19.8 + - - +
75B GLU 3.6 8.4 - - - +
76B CYS* 3.5 24.2 + - - +
77B ASP* 3.7 16.1 - - - +
124B SER* 3.5 31.5 + - - -
125B LEU 3.3 8.7 - - - +
126B THR* 4.0 17.0 + - + +
127B PHE* 4.4 0.9 - - - -
153B TRP 4.8 0.2 - - - -
154B CYS* 3.5 1.8 - - - -
155B ASN* 2.7 46.3 + - - +
156B GLY 4.6 0.9 + - - -
182B ASN* 1.3 77.1 - - - +
184B LEU* 1.4 68.0 - - - +
185B ALA* 4.2 5.0 + - + +
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Residues in contact with LEU 184 (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 LEU* 3.9 17.7 - - + -
58B TRP* 4.1 18.4 - - + -
124B SER* 3.1 9.8 - - - -
125B LEU* 2.9 35.0 + - + +
127B PHE* 3.4 23.3 - - + -
141B ILE* 3.3 27.8 - - + -
143B PHE* 4.8 1.8 - - + -
152B LEU* 4.4 13.9 - - + -
153B TRP 3.6 3.8 - - - +
154B CYS* 4.2 11.9 - - + -
173B LEU* 3.9 27.4 - - + -
183B ARG* 1.4 75.9 - - - +
185B ALA* 1.4 59.9 + - - +
186B VAL* 4.9 4.7 - - + -
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Residues in contact with ALA 185 (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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73B TRP* 3.6 38.4 - - + +
74B LEU* 4.4 7.2 - - + +
123B TYR 3.5 4.7 - - - -
124B SER* 4.4 0.9 - - - -
152B LEU* 3.5 2.1 - - - +
153B TRP* 2.9 49.7 + - + +
183B ARG* 4.2 7.4 + - - +
184B LEU* 1.4 73.9 - - - +
186B VAL* 1.3 63.6 + - - +
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Residues in contact with VAL 186 (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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58B TRP* 4.1 18.2 - - + -
73B TRP* 3.7 3.4 - - - -
121B GLY 3.3 3.6 - - - +
123B TYR* 2.8 34.9 + - + +
143B PHE* 3.9 27.4 - - + -
146B VAL* 5.3 0.4 - - + -
150B PHE* 3.7 31.9 - - + -
151B HIS 3.5 3.4 - - - +
152B LEU* 4.0 6.7 - - + -
184B LEU* 4.9 2.2 - - + -
185B ALA* 1.3 80.0 - - - +
187B MET* 1.3 62.2 + - - +
188B VAL* 4.0 17.3 - - + -
208B ILE* 4.1 14.6 - - + -
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Residues in contact with MET 187 (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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16B TRP* 5.0 5.6 - - + -
66B PRO* 4.1 23.6 - - + +
69B VAL* 4.3 13.5 - - - -
73B TRP* 3.8 10.0 - - + -
120B THR* 3.4 29.4 - - + -
121B GLY 3.6 3.1 - - - -
122B CYS* 4.4 7.9 - - - -
150B PHE* 3.2 5.6 - - - -
151B HIS* 3.0 58.3 + - + +
153B TRP* 3.7 25.5 - - + -
186B VAL* 1.3 73.0 - - - +
188B VAL* 1.3 60.6 + - - +
189B LEU* 3.9 10.9 + - + +
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Residues in contact with VAL 188 (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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90B TRP* 3.5 17.8 - - + -
120B THR* 3.3 6.0 - - - -
121B GLY 2.8 39.4 + - - +
123B TYR* 3.6 27.4 - - + -
146B VAL* 3.8 29.6 - - + -
147B ASN 3.3 26.2 - - - +
149B ALA 3.4 6.1 - - - +
150B PHE* 4.2 0.2 - - + -
186B VAL* 4.0 9.0 - - + -
187B MET* 1.3 75.8 - - - +
189B LEU* 1.3 63.4 + - - +
207B GLY 4.1 4.0 - - - +
208B ILE* 3.9 7.2 - - + -
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Residues in contact with LEU 189 (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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16B TRP* 3.2 53.6 - - + -
66B PRO* 4.0 24.2 - - + -
118B ASN* 4.1 8.1 - - - +
119B PRO 4.0 0.9 - - - -
120B THR* 3.8 22.2 - - + +
148B SER* 3.0 23.0 + - - -
149B ALA* 2.9 22.9 + - + +
150B PHE* 5.5 0.7 - - - -
151B HIS* 5.4 0.9 - - + -
161B TYR* 5.1 4.5 - - + +
187B MET* 4.6 13.0 - - + +
188B VAL* 1.3 74.0 - - - +
190B ARG* 1.3 65.7 + - - +
191B TRP 3.5 13.7 - - - +
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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