Contacts of the strand formed by residues 138 - 143 (chain A) 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 GLN 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A LEU* 4.7 8.9 - - - +
137A GLY* 1.3 76.6 - - - -
139A THR* 1.3 68.7 + - - +
140A ARG* 3.0 35.4 + - + +
172A ASP* 3.0 36.0 + - - +
174A SER* 3.2 5.2 - - - +
215A LEU 3.4 1.6 - - - +
216A HIS* 3.3 6.3 + - - -
217A LYS* 2.6 43.5 + - - +
218A PRO 5.0 1.3 - - - +
219A THR* 5.4 2.7 - - - +
221A GLN* 3.2 22.2 + - - +
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Residues in contact with THR 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A VAL* 5.4 1.3 - - + -
133A TRP* 3.4 47.6 + - + +
134A LEU* 4.1 5.7 - - - +
137A GLY 4.4 0.4 + - - -
138A GLN* 1.3 72.9 - - - +
140A ARG* 1.4 55.8 + - - +
172A ASP* 3.2 2.1 - - - +
173A LEU* 2.7 32.1 + - - -
174A SER* 2.8 13.6 + - - -
177A LEU* 3.7 28.3 - - + -
214A LEU* 4.0 21.5 - - + -
215A LEU 3.5 2.7 - - - -
216A HIS* 3.6 7.3 - - - -
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Residues in contact with ARG 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 3.7 26.8 - - + +
28A ALA 4.7 0.2 + - - -
30A HIS* 3.4 18.4 + - - -
33A PHE* 5.3 2.0 - - - -
138A GLN* 3.0 32.3 + - + +
139A THR* 1.4 75.9 - - - +
141A ILE* 1.3 63.1 + - - +
142A ILE* 3.9 11.2 - - + -
170A GLU* 2.7 38.6 + - - -
171A PHE 3.2 18.2 - - - +
172A ASP* 4.2 2.5 - - - -
173A LEU* 4.8 0.9 - - - -
214A LEU* 3.4 9.4 - - - +
215A LEU* 3.0 67.6 + - + +
217A LYS* 4.2 12.2 - - - +
221A GLN* 3.8 13.7 + - - -
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Residues in contact with ILE 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LEU* 4.1 8.1 - - + -
140A ARG* 1.3 76.7 - - - +
142A ILE* 1.3 67.9 + - - +
143A PHE* 3.5 28.7 - - + -
152A LEU* 4.1 9.4 - - + -
169A SER 3.9 0.5 - - - +
170A GLU* 3.2 5.4 - - - +
171A PHE* 2.9 46.6 + - + +
173A LEU* 3.6 26.3 - - + +
184A LEU* 3.5 36.6 - - + -
212A VAL* 3.9 11.0 - - + -
213A SER 3.5 10.8 - - - +
214A LEU* 4.0 3.1 - - + -
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Residues in contact with ILE 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A HIS* 5.4 2.5 - - + +
33A PHE 6.1 0.2 - - - +
51A LEU* 5.3 3.8 - - + -
140A ARG* 3.9 16.4 - - + +
141A ILE* 1.3 81.2 - - - +
143A PHE* 1.3 64.6 + - - +
144A ASP* 3.9 22.2 - - - +
168A PRO* 4.1 5.2 - - + -
169A SER 3.5 2.5 - - - -
170A GLU* 3.7 40.2 - - + +
211A ASP 3.8 0.9 - - - +
212A VAL* 3.4 4.9 - - - +
213A SER* 2.8 51.3 + - - +
215A LEU* 4.2 21.5 - - + -
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Residues in contact with PHE 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A TRP* 4.1 6.1 - + - -
141A ILE* 3.5 38.8 - - + -
142A ILE* 1.3 72.6 - - - +
144A ASP* 1.3 65.1 + - - +
145A GLY* 3.2 2.2 + - - +
146A VAL* 3.8 29.5 + - + +
150A PHE* 4.2 19.7 - + + -
152A LEU* 4.0 19.5 - - + -
167A LEU 4.1 1.2 - - - +
168A PRO* 3.2 0.8 - - - +
169A SER* 2.8 43.4 + - - +
171A PHE* 4.6 2.0 - + - -
184A LEU* 4.4 3.4 - - + -
186A VAL* 3.8 32.5 - - + -
208A ILE* 4.2 8.3 - - + -
211A ASP 3.9 3.4 - - - -
212A VAL* 3.8 28.5 - - + +
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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