Contacts of the helix formed by residues 98 - 109 (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 SER 98 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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977 GLU* 3.1 34.9 + - - -
97T MET* 1.3 75.9 - - - +
99T ILE* 1.3 65.5 + - - +
100T ASP 3.5 1.7 + - - -
101T GLN* 3.0 23.2 + - - +
102T ALA* 2.9 18.6 + - - +
138T SER 4.9 1.8 - - - -
140T LEU 3.7 9.9 - - - -
141T TYR* 3.9 5.6 - - - +
183T PRO* 4.1 20.9 - - - +
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Residues in contact with ILE 99 (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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97T MET 3.7 1.4 + - - -
98T SER* 1.3 70.3 - - - +
100T ASP* 1.3 58.0 + - - +
102T ALA* 3.2 3.6 + - - +
103T LEU* 2.8 51.9 + - + +
121T LEU* 4.7 6.7 - - + +
125T GLN* 3.2 36.8 - - + +
140T LEU* 2.8 54.0 + - + +
142T ILE* 4.1 11.4 - - + -
178T LEU* 3.4 42.0 - - + -
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Residues in contact with ASP 100 (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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1160 LEU* 6.1 0.2 - - - +
967 SER* 3.5 12.3 - - - -
977 GLU* 2.7 48.4 + - + +
987 TRP* 4.2 17.7 + - + +
98T SER* 3.1 3.3 - - - +
99T ILE* 1.3 88.8 + - - +
101T GLN* 1.3 57.5 + - - +
103T LEU* 3.2 9.8 + - - +
104T ALA* 2.9 28.8 + - - +
125T GLN* 4.0 7.5 + - - -
137T ARG* 5.9 0.2 - - - +
138T SER* 3.6 21.0 - - - +
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Residues in contact with GLN 101 (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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1030 VAL* 3.9 18.4 - - - +
1040 LYS 5.7 0.2 + - - -
977 GLU* 4.8 5.8 + - - +
987 TRP* 5.2 7.4 - - + +
97T MET* 3.3 45.4 - - - +
98T SER* 3.0 18.8 + - - +
100T ASP* 1.3 79.1 - - - +
102T ALA* 1.3 57.5 + - - +
104T ALA* 3.2 8.9 + - + +
105T GLN* 2.9 39.7 + - + +
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Residues in contact with ALA 102 (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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94T ILE* 3.8 16.1 - - + +
97T MET* 3.5 18.1 - - + +
98T SER 2.9 8.1 + - - +
99T ILE 3.4 4.9 - - - +
101T GLN* 1.3 77.7 - - - +
103T LEU* 1.3 56.8 - - - +
105T GLN* 3.2 3.6 + - - +
106T LEU* 2.9 34.8 + - - +
121T LEU* 4.1 5.6 - - + -
142T ILE* 3.4 33.7 - - + -
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Residues in contact with LEU 103 (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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1160 LEU* 5.7 2.2 - - + -
99T ILE* 2.8 32.9 + - + +
100T ASP* 3.4 11.9 - - - +
102T ALA* 1.3 77.3 - - - +
104T ALA* 1.3 57.6 + - - +
106T LEU* 3.2 4.1 + - - +
107T GLU* 2.9 37.5 + - + +
118T LYS* 4.1 24.0 - - + +
121T LEU* 3.4 38.6 - - + -
122T LEU* 3.7 25.6 - - + -
125T GLN* 4.3 7.6 - - - +
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Residues in contact with ALA 104 (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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1070 ILE* 3.6 16.6 - - + +
1160 LEU* 4.1 20.8 - - + +
987 TRP* 3.8 27.6 - - + +
100T ASP 2.9 12.8 + - - +
101T GLN* 3.2 10.1 + - + +
103T LEU* 1.3 76.9 - - - +
105T GLN* 1.3 63.2 + - - +
107T GLU* 3.3 9.3 + - - -
108T PHE* 3.3 21.0 - - - -
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Residues in contact with GLN 105 (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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1020 LYS 4.0 3.8 - - - +
1030 VAL* 3.4 16.7 - - - +
1040 LYS* 3.1 52.7 + - - +
1070 ILE* 3.2 27.6 - - - +
93T LEU* 3.9 23.9 - - + +
97T MET* 3.7 17.5 - - + -
101T GLN* 2.9 25.9 + - - +
102T ALA 3.2 7.8 + - - +
104T ALA* 1.3 76.5 - - - +
106T LEU* 1.3 62.8 + - - +
108T PHE* 3.2 3.8 + - - +
109T ASN* 3.0 24.5 + - - +
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Residues in contact with LEU 106 (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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90T LEU* 4.2 12.6 - - + -
93T LEU* 4.6 6.1 - - + -
94T ILE* 3.7 21.1 - - + -
102T ALA 2.9 16.4 + - - +
103T LEU 3.2 6.9 + - - +
105T GLN* 1.3 74.3 - - - +
107T GLU* 1.3 67.0 + - - +
108T PHE 3.1 1.2 + - - -
109T ASN* 3.2 19.6 + - + +
114T ALA* 3.8 37.4 - - + +
117T ILE* 3.6 8.7 - - + -
118T LYS* 3.5 34.5 - - + +
121T LEU* 3.5 31.6 - - + -
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Residues in contact with GLU 107 (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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1150 HIS* 4.1 11.2 - - - +
1160 LEU* 3.4 33.7 - - + +
103T LEU* 2.9 19.7 + - - +
104T ALA 3.5 4.5 - - - +
105T GLN 3.3 0.4 - - - -
106T LEU* 1.3 77.7 - - - +
108T PHE* 1.3 86.1 + - + +
109T ASN 3.9 2.1 + - - +
110T ASP* 5.8 0.5 - - - +
118T LYS* 3.5 34.9 + - + +
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Residues in contact with PHE 108 (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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1040 LYS* 3.5 28.4 + - + -
1070 ILE* 4.5 8.7 - - + -
1160 LEU* 3.5 23.3 - - + -
1170 LYS* 3.5 25.4 - - + -
1180 GLN* 3.3 58.5 + - + +
1210 VAL* 6.1 1.6 - - + -
1240 ALA* 6.5 0.9 - - + -
104T ALA 3.3 11.0 - - - +
105T GLN 3.2 3.3 + - - +
106T LEU 3.1 0.4 - - - -
107T GLU* 1.3 101.5 - - + +
109T ASN* 1.3 63.1 + - - +
110T ASP* 3.4 14.7 + - - +
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Residues in contact with ASN 109 (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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1010 ILE* 3.2 32.4 - - - +
1020 LYS 5.3 0.2 + - - -
1040 LYS* 4.7 9.7 - - - +
117O ARG* 5.3 2.4 + - - -
90T LEU* 3.2 27.3 - - + +
93T LEU* 4.5 6.7 - - + +
105T GLN 3.0 16.1 + - - +
106T LEU* 3.2 15.5 + - + +
107T GLU 4.7 2.0 - - - +
108T PHE* 1.3 75.9 - - - +
110T ASP* 1.3 62.4 + - - +
111T LYS* 2.9 30.5 + - - +
114T ALA* 3.6 11.4 - - + +
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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