Contacts of the helix formed by residues 96 - 109 (chain L) in PDB entry 1JJ2
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 ASN 96 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4010 C 3.4 34.8 + - - +
4020 U 3.3 17.9 - - - +
95L LYS* 1.3 74.8 - - - +
97L ILE* 1.3 60.6 + - - +
98L GLN* 3.8 25.9 + - - +
99L ARG* 2.9 36.7 + - - +
100L ILE* 3.1 10.2 + - - +
166L ALA* 4.5 8.1 + - - +
169L ARG* 5.8 1.6 - - - +
170L CYS* 3.6 16.1 - - - +
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Residues in contact with ILE 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4020 U 2.8 28.0 + - - +
4030 C 4.0 11.2 - - - +
67L ILE* 3.5 27.6 - - + -
68L ARG* 3.6 35.2 - - - +
69L LYS* 4.1 1.3 - - - -
70L GLY 4.4 2.0 - - - +
95L LYS 3.9 0.6 + - - +
96L ASN* 1.3 71.8 - - - +
98L GLN* 1.3 64.6 + - - +
100L ILE* 3.0 13.2 + - + +
101L ALA* 2.9 21.0 + - - +
127L LYS* 3.6 35.7 - - + +
129L HIS* 4.0 16.2 - - + -
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Residues in contact with GLN 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96L ASN* 3.2 15.9 + - - +
97L ILE* 1.3 77.3 - - - +
99L ARG* 1.3 58.2 + - - +
101L ALA* 3.2 4.5 + - - +
102L GLU* 3.0 27.7 + - - +
117L SER* 2.6 48.1 + - - +
118L TYR* 3.8 5.2 - - - +
119L SER* 5.3 1.1 + - - -
129L HIS* 3.5 34.0 + - + +
165L SER* 5.0 1.6 + - - -
166L ALA* 3.9 21.0 - - + +
169L ARG* 4.5 10.9 + - - +
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Residues in contact with ARG 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1560 C 3.3 23.0 + - - -
1570 G 2.7 33.7 + - - -
95L LYS* 3.7 23.7 - - + +
96L ASN* 2.9 18.8 + - - +
98L GLN* 1.3 78.9 - - - +
100L ILE* 1.3 64.6 + - - +
102L GLU* 3.2 15.6 + - + +
103L GLU* 3.1 27.5 + - + +
159L THR* 4.3 9.3 + - + +
162L GLY* 3.8 19.2 - - - -
164L THR* 4.8 0.7 - - - -
166L ALA* 3.7 7.0 - - - -
167L GLY* 3.3 36.7 + - - +
170L CYS* 3.2 27.0 - - - +
171L ARG* 4.4 0.4 - - - +
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Residues in contact with ILE 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14700 A 3.6 41.5 - - - +
14710 A 3.4 23.6 - - - +
67L ILE* 3.8 17.3 - - + -
68L ARG* 4.8 8.1 - - - +
93L ARG* 5.6 1.3 - - + -
95L LYS* 4.4 18.2 - - + +
96L ASN 3.1 10.0 + - - +
97L ILE* 3.0 21.5 + - + +
99L ARG* 1.3 75.8 - - - +
101L ALA* 1.3 64.9 + - - +
103L GLU* 3.2 8.2 + - - +
104L ARG* 3.0 38.3 + - - +
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Residues in contact with ALA 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65L VAL* 3.6 16.6 - - + +
67L ILE* 3.8 23.7 - - + +
97L ILE 2.9 12.0 + - - +
98L GLN 3.2 11.2 - - - +
100L ILE* 1.3 77.5 - - - +
102L GLU* 1.3 61.5 + - - +
104L ARG* 3.4 1.0 + - - +
105L ALA* 3.1 24.1 + - - +
129L HIS* 4.1 25.8 - - + +
131L VAL* 4.4 3.6 - - + -
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Residues in contact with GLU 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98L GLN* 3.0 21.6 + - - +
99L ARG* 3.2 11.6 + - + +
101L ALA* 1.3 75.7 - - - +
103L GLU* 1.3 58.2 + - - +
105L ALA* 3.5 1.9 + - - +
106L ASN* 3.0 29.3 + - - +
114L VAL* 3.9 12.2 - - + +
116L ASN 3.9 1.4 - - - -
117L SER* 2.5 40.0 + - - +
131L VAL* 4.1 10.3 - - + -
159L THR* 3.8 14.7 - - + +
164L THR* 2.6 37.6 + - - +
165L SER* 3.3 16.5 + - - -
166L ALA* 4.2 7.7 - - - +
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Residues in contact with GLU 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1560 C 4.7 4.0 + - - -
14700 A 4.5 0.8 + - - -
14710 A 4.3 9.4 - - - +
95L LYS* 3.0 37.8 + - - +
99L ARG* 3.1 17.5 + - + +
100L ILE* 3.2 8.7 + - - +
102L GLU* 1.3 75.2 - - - +
104L ARG* 1.3 60.6 + - + +
106L ASN* 3.2 4.7 + - - +
107L ARG* 2.9 64.8 + - - +
159L THR* 4.2 21.0 - - - +
160L PHE* 3.8 26.4 - - + +
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Residues in contact with ARG 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14680 G 4.3 16.6 + - - -
14690 C 2.9 51.5 + - - +
14700 A 5.0 2.8 + - - -
14710 A 2.8 40.3 + - - +
36L ALA* 5.8 4.2 - - - +
37L VAL* 4.1 2.2 - - + -
65L VAL* 4.2 11.4 - - + -
66L ALA 3.8 8.4 + - - -
67L ILE* 3.1 40.0 - - - +
68L ARG* 4.9 2.4 - - - +
100L ILE* 3.0 23.2 + - - +
101L ALA 3.4 4.0 + - - +
103L GLU* 1.3 76.2 - - + +
105L ALA* 1.3 59.9 + - - +
107L ARG* 3.4 5.6 + - - +
108L LYS* 2.8 49.0 + - - +
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Residues in contact with ALA 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L VAL* 4.1 15.9 - - + -
63L VAL* 4.9 2.2 - - + -
65L VAL* 3.6 21.9 - - + +
101L ALA 3.1 11.2 + - - +
102L GLU 3.7 4.0 - - - +
104L ARG* 1.3 76.0 - - - +
106L ASN* 1.3 65.2 + - - +
108L LYS* 2.9 12.5 + - - +
109L PHE* 3.1 20.0 - - + -
131L VAL* 3.9 22.2 - - + -
133L LEU* 4.2 9.0 - - + -
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Residues in contact with ASN 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102L GLU 3.0 18.2 + - - +
103L GLU 3.5 4.3 - - - +
105L ALA* 1.3 79.0 - - - +
107L ARG* 1.3 61.0 + - - +
109L PHE 3.1 11.4 - - - -
110L PRO* 3.5 0.7 - - - +
112L LEU 3.5 5.7 + - - -
113L ARG 4.2 0.2 - - - -
114L VAL* 3.2 15.3 - - + +
133L LEU* 4.0 9.5 - - - +
157L LEU* 4.5 0.9 - - - +
159L THR* 3.7 4.5 - - - +
160L PHE* 2.9 26.1 - - + -
8347L NA 2.4 44.5 - - - -
8518L CL 2.4 36.5 - - - +
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Residues in contact with ARG 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1330 U 4.5 1.4 + - - -
1810 G 3.3 30.5 + - - -
14710 A 3.4 39.1 + - - -
14720 C 3.2 25.4 + - - -
103L GLU* 2.9 46.0 + - - +
104L ARG* 3.9 8.4 - - - +
105L ALA 3.2 0.2 - - - -
106L ASN* 1.3 77.2 - - - +
108L LYS* 1.3 75.4 + - - +
110L PRO* 3.3 16.4 - - - +
160L PHE* 3.4 25.9 - - + -
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Residues in contact with LYS 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1330 U 2.7 26.4 + - - +
1340 U 3.6 13.6 - - - +
14670 C 6.1 0.9 - - - -
14690 C 5.0 9.3 - - - +
14720 C 5.5 2.2 + - - -
36L ALA* 5.7 4.7 - - - -
37L VAL* 3.2 39.7 - - + -
104L ARG* 2.8 40.8 - - - +
105L ALA 2.9 6.4 + - - +
107L ARG* 1.3 92.5 - - - +
109L PHE* 1.3 63.9 + - + +
110L PRO* 3.1 0.4 - - - +
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Residues in contact with PHE 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1340 U 3.3 41.3 - - - +
1350 G 3.9 9.0 - - - -
37L VAL* 3.8 16.8 - - + -
39L ARG* 4.2 12.8 - - + -
61L ILE* 4.5 7.0 - - + -
63L VAL* 3.3 38.1 - - + -
105L ALA 3.1 23.6 - - - -
106L ASN 3.1 6.1 + - - +
108L LYS* 1.3 82.0 - - + +
110L PRO* 1.3 58.5 - - - +
111L ASN* 3.2 3.6 - - - -
112L LEU* 2.9 38.6 + - + +
133L LEU* 3.8 14.1 - - + -
8347L NA 2.7 19.6 - - - -
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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
------------------------------------------------------------
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