Contacts of the strand formed by residues 140 - 149 (chain T) in PDB entry 3J7Y
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 LEU 140 (chain T).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73T ILE* 4.3 11.2 - - + -
98T SER* 3.7 2.8 - - - -
99T ILE* 2.8 52.0 + - + +
125T GLN* 3.9 13.9 - - + +
128T ALA* 3.8 28.5 - - + -
129T VAL* 5.8 0.9 - - + -
134T VAL* 3.9 23.8 - - + -
136T PHE 4.2 2.0 - - - +
137T ARG* 3.1 21.6 + - + +
138T SER 4.1 4.9 - - - +
139T ASN* 1.3 76.6 - - - +
141T TYR* 1.3 60.3 + - - +
178T LEU* 4.3 11.0 - - + -
179T VAL 3.5 17.0 - - - +
180T GLU* 4.5 2.0 - - - +
183T PRO* 6.1 0.2 - - - -
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Residues in contact with TYR 141 (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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96T GLY* 4.1 7.6 - - - -
97T MET 3.6 9.9 - - - +
98T SER* 3.9 2.9 - - - +
99T ILE 4.1 0.4 - - - +
139T ASN 3.7 0.6 + - - -
140T LEU* 1.3 76.1 - - - +
142T ILE* 1.3 70.8 + - - +
143T ALA* 3.3 28.6 + - + +
178T LEU* 3.3 3.9 - - - -
179T VAL* 2.8 69.1 + - + +
180T GLU 4.6 2.0 - - - -
181T GLY 3.3 22.0 - - - +
182T PRO 4.1 1.8 - - - -
183T PRO* 3.7 23.3 - - + -
184T PRO* 3.3 38.1 - - + +
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Residues in contact with ILE 142 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94T ILE* 3.3 36.3 - - + -
95T ARG 2.4 36.2 - - - +
96T GLY* 3.9 2.8 - - - -
97T MET 2.8 18.3 + - - +
99T ILE* 4.1 9.6 - - + -
102T ALA* 3.4 22.7 - - + -
121T LEU* 3.6 17.7 - - + -
141T TYR* 1.3 80.4 - - - +
143T ALA* 1.3 58.3 + - - +
144T GLU 3.5 26.7 - - - +
145T SER* 4.2 4.9 - - - -
174T TYR* 5.6 0.2 - - - +
176T VAL* 4.7 3.6 - - + -
177T LYS 3.6 4.5 - - - +
178T LEU* 3.4 21.8 - - + -
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Residues in contact with ALA 143 (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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95T ARG* 4.4 7.3 - - - +
141T TYR* 3.3 22.6 + - - +
142T ILE* 1.3 74.5 - - - +
144T GLU* 1.3 66.4 + - + +
177T LYS* 2.8 24.9 + - + +
179T VAL* 3.6 30.5 - - + -
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Residues in contact with GLU 144 (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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1819A U 3.6 26.6 + - - +
1820A A 4.6 4.7 + - - -
51T TRP* 3.6 24.0 - - + -
95T ARG* 4.9 2.7 - - - -
142T ILE* 3.5 8.4 - - - +
143T ALA* 1.3 85.8 - - + +
145T SER* 1.3 63.9 + - - +
146T THR* 5.6 6.3 - - + +
176T VAL* 3.6 1.1 - - - -
177T LYS* 2.8 60.5 + - + +
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Residues in contact with SER 145 (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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91T ALA* 2.6 33.8 + - - +
94T ILE* 4.7 1.8 - - - -
95T ARG* 2.8 37.4 + - - +
142T ILE* 4.2 9.2 - - - -
144T GLU* 1.3 77.8 - - - +
146T THR* 1.3 62.5 + - - +
174T TYR* 3.4 27.8 - - - -
175T PHE 3.3 6.5 - - - -
176T VAL* 5.0 0.7 - - - -
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Residues in contact with THR 146 (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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1818A A 3.5 13.9 - - - +
1819A U 3.5 37.0 - - - -
51T TRP* 5.3 4.5 - - - -
91T ALA* 4.5 3.4 - - - -
95T ARG* 3.5 6.3 - - - +
144T GLU* 5.5 7.4 - - + +
145T SER* 1.3 80.1 - - - +
147T SER* 1.3 60.9 + - - +
173T HIS 3.8 0.3 - - - +
174T TYR* 3.4 7.5 - - - -
175T PHE* 2.8 58.2 + - - +
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Residues in contact with SER 147 (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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1671A G 5.4 0.7 + - - -
1817A C 5.6 1.0 + - - -
1818A A 4.5 18.7 + - - +
84T LYS* 3.0 28.3 + - - +
87T MET* 3.5 32.3 - - - -
88T TRP* 3.4 21.2 + - - +
91T ALA* 5.0 0.8 - - - +
146T THR* 1.3 76.3 - - - +
148T GLY* 1.3 60.7 + - - +
172T CYS* 5.3 0.2 - - - -
173T HIS 3.4 7.4 - - - -
174T TYR* 4.8 1.3 - - - +
175T PHE* 5.3 0.7 - - - -
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Residues in contact with GLY 148 (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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1671A G 4.9 7.0 - - - -
1672A C 3.6 18.4 - - - -
84T LYS* 4.1 5.3 - - - +
146T THR 4.2 0.6 - - - -
147T SER* 1.3 74.5 - - - +
149T ARG* 1.3 59.2 + - - -
172T CYS* 3.3 8.3 - - - +
173T HIS* 2.8 38.0 + - - +
175T PHE* 4.5 8.5 - - - -
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Residues in contact with ARG 149 (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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1672A C 2.5 28.5 + - - +
1673A U 3.3 47.3 + - - +
1674A A 4.8 1.0 + - - -
1816A G 4.4 13.0 - - - +
2305A U 3.1 40.2 + - - -
2306A A 3.2 30.3 + - - -
84T LYS* 3.6 32.7 - - + +
148T GLY* 1.3 71.3 - - - -
150T GLY* 1.3 70.8 + - - +
152T CYS* 3.7 27.8 - - - +
168T GLU* 4.9 5.9 + - - +
170T VAL* 5.9 2.0 - - + -
171T TYR 3.7 7.2 - - - +
173T HIS* 3.6 1.8 - - - -
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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