Contacts of the strand formed by residues 135 - 140 (chain T) in PDB entry 1V2J
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 135 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133T GLY 3.4 8.7 + - - +
134T THR* 1.3 77.3 - - - +
136T CYS* 1.3 65.4 + - - +
159T LYS* 4.1 12.8 - - + +
160T ALA 3.7 15.8 + - - +
161T PRO* 3.5 20.0 - - - +
184T TYR* 3.9 17.3 - - - -
201T CYS* 3.7 12.3 - - - +
202T SER 4.7 2.1 + - - -
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Residues in contact with CYS 136 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134T THR 3.7 3.1 - - - -
135T GLN* 1.3 77.2 - - - +
137T LEU* 1.3 60.3 + - - +
138T ILE* 4.1 2.9 - - + -
158T LEU 3.6 0.5 - - - +
159T LYS* 3.2 7.8 - - - +
160T ALA* 2.6 43.3 + - - +
162T ILE* 3.7 27.1 - - - -
199T VAL* 3.8 17.3 - - + -
200T VAL 3.3 5.4 - - - +
201T CYS* 2.0 46.9 - - - -
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Residues in contact with LEU 137 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20T TYR* 3.6 24.0 - - - +
26T THR 5.8 0.9 - - - +
27T VAL* 4.5 11.2 - - + -
29T TYR* 4.1 20.6 + - - +
136T CYS* 1.3 74.0 - - - +
138T ILE* 1.3 63.6 + - - +
139T SER* 4.4 2.2 + - - -
157T CYS* 4.0 26.5 - - + -
158T LEU 3.5 13.7 - - - +
159T LYS* 4.4 6.3 - - + -
198T PRO* 3.6 2.6 - - - +
199T VAL* 3.5 2.6 - - - -
200T VAL* 2.7 39.7 + - + +
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Residues in contact with ILE 138 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16T ILE* 4.1 14.9 - - + +
136T CYS* 4.7 3.1 - - + +
137T LEU* 1.3 78.5 - - - +
139T SER* 1.3 66.2 + - - +
157T CYS* 3.5 1.2 - - - -
158T LEU* 2.8 50.5 + - + +
160T ALA* 3.8 28.0 - - + +
183T ALA* 4.9 5.8 - - + -
184T GLY* 6.1 0.2 - - - -
190T SER* 4.3 6.1 - - - -
198T PRO 3.5 11.4 - - - +
199T VAL* 4.1 17.0 - - + -
213T VAL* 4.0 22.4 - - + -
228T TYR* 3.5 27.6 - - + +
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Residues in contact with SER 139 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16T ILE* 4.1 8.7 - - - +
22T CYS* 4.3 3.1 - - - -
27T VAL* 3.7 14.8 - - - +
29T TYR* 5.1 0.7 + - - -
30T GLN* 2.7 33.1 + - - +
137T LEU* 5.2 3.1 + - - +
138T ILE* 1.3 80.9 - - - +
140T GLY* 1.3 58.9 + - - +
155T LEU* 4.4 5.4 - - - -
156T LYS 3.2 14.6 - - - -
157T CYS* 4.0 15.7 - - - -
194T ASP* 4.4 4.7 - - - +
197T GLY* 4.6 5.9 - - - -
198T PRO* 3.7 16.7 + - - +
213T VAL* 5.1 0.2 - - - +
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Residues in contact with GLY 140 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16T ILE* 3.9 3.0 - - - +
30T GLN* 4.3 7.2 - - - -
139T SER* 1.3 76.6 - - - +
141T TRP* 1.3 59.2 + - - -
142T GLY 3.4 0.6 + - - -
155T LEU* 3.6 16.2 - - - +
156T LYS* 3.0 35.9 + - - +
194T ASP* 3.3 19.4 - - - +
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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