Contacts of the strand formed by residues 60 - 68 (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 ILE 60 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1360 C 5.1 1.4 + - - -
39L ARG* 4.8 4.9 + - - -
53L GLY 4.9 0.2 - - - +
54L TYR* 3.8 26.9 - - + -
55L LYS* 2.9 53.8 - - + +
57L LYS* 3.4 25.3 + - + +
58L GLN 3.3 1.0 - - - -
59L GLY* 1.3 80.7 + - - +
61L ILE* 1.3 69.1 + - - +
62L VAL* 5.6 0.3 - - - +
132L ILE* 4.5 6.7 - - + -
133L LEU 3.8 2.9 - - - +
134L ILE* 3.7 21.1 - - + -
141L ILE* 4.4 7.2 - - + -
147L LEU* 3.9 17.5 - - + -
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Residues in contact with ILE 61 (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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1350 G 3.5 30.3 - - - +
1360 C 4.5 1.6 - - - +
39L ARG* 3.9 33.2 - - - +
59L GLY* 3.5 20.2 - - - +
60L ILE* 1.3 83.2 - - - +
62L VAL* 1.3 69.7 - - - +
63L VAL* 3.8 22.4 - - + -
109L PHE* 4.5 3.8 - - + -
112L LEU* 3.9 30.5 - - + -
132L ILE* 3.4 5.7 - - - +
133L LEU* 2.7 41.7 + - + +
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Residues in contact with VAL 62 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39L ARG* 3.6 4.4 - - - +
40L ILE* 3.1 54.4 + - + +
41L GLU 5.8 1.6 - - - +
43L PRO* 3.9 18.4 - - + -
54L TYR* 3.7 36.1 - - + -
60L ILE 5.6 0.2 - - - +
61L ILE* 1.3 80.6 - - - +
63L VAL* 1.3 72.1 + - - +
118L TYR* 4.6 2.2 - - - +
130L GLU* 4.3 13.9 - - + -
131L VAL 3.3 9.9 - - - +
132L ILE* 4.6 10.1 - - + -
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Residues in contact with VAL 63 (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* 3.1 33.0 - - + -
38L VAL 2.9 26.7 - - - +
39L ARG* 3.5 4.0 - - - +
40L ILE* 4.4 1.1 - - - +
61L ILE* 3.8 10.5 - - + -
62L VAL* 1.3 84.3 - - - +
64L ARG* 1.3 61.5 + - - +
65L VAL* 3.9 1.6 + - + +
105L ALA* 4.9 3.4 - - + -
109L PHE* 3.3 32.5 - - + -
129L HIS 3.6 0.7 - - - +
130L GLU* 3.2 5.1 - - - -
131L VAL* 2.7 39.2 + - - +
133L LEU* 4.0 8.7 - - + -
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Residues in contact with ARG 64 (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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55F GLN* 5.5 5.3 - - - +
31L TRP* 3.1 50.7 - - - +
34L GLU* 2.9 29.9 + - - -
35L PRO 5.2 1.2 - - - +
36L ALA 3.7 1.2 - - - +
37L VAL* 3.7 1.4 - - - -
38L VAL* 3.0 36.0 + - + +
40L ILE* 3.5 29.4 - - + +
44L THR* 3.8 9.5 + - - -
63L VAL* 1.3 72.1 - - - +
65L VAL* 1.3 61.6 + - - +
66L ALA 4.3 0.2 + - - -
120L VAL* 4.4 0.9 - - + -
128L TRP* 3.8 25.8 - - + -
129L HIS 3.3 9.0 - - - +
130L GLU* 3.3 30.2 + - + +
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Residues in contact with VAL 65 (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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36L ALA 3.1 9.9 - - - +
37L VAL* 4.0 13.9 - - + -
63L VAL* 4.4 2.0 - - + +
64L ARG* 1.3 78.6 - - - +
66L ALA* 1.3 72.4 + - - +
67L ILE* 3.8 19.0 - - + +
101L ALA* 3.6 20.6 - - + +
104L ARG* 4.2 11.7 - - + -
105L ALA* 3.6 31.2 - - + -
127L LYS 3.6 1.2 - - - +
128L TRP* 3.4 8.4 - - - -
129L HIS* 2.8 34.4 + - - +
131L VAL* 4.2 8.5 - - + -
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Residues in contact with ALA 66 (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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14680 G 4.4 9.8 + - - +
35L PRO 4.5 10.3 + - - +
36L ALA* 3.0 18.6 + - - +
64L ARG 4.3 0.4 + - - -
65L VAL* 1.3 72.5 - - - +
67L ILE* 1.3 75.0 + - - +
104L ARG* 3.8 6.1 + - - -
126L HIS* 3.9 18.6 - - + -
127L LYS 3.5 4.9 - - - +
128L TRP* 3.7 22.4 - - + +
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Residues in contact with ILE 67 (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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14680 G 5.7 0.7 - - - -
65L VAL* 3.8 9.2 - - + +
66L ALA* 1.3 84.3 - - - +
68L ARG* 1.3 84.2 + - - +
97L ILE* 3.5 25.6 - - + -
100L ILE* 3.8 20.4 - - + -
101L ALA* 3.8 25.6 - - + +
104L ARG* 3.1 47.8 - - - +
126L HIS* 3.5 4.1 - - - -
127L LYS* 2.9 35.5 + - - +
129L HIS* 5.4 0.4 - - - +
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Residues in contact with ARG 68 (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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14680 G 5.9 0.6 + - - -
14690 C 3.2 30.6 + - - +
14700 A 2.8 45.8 + - - -
67L ILE* 1.3 82.6 - - - +
69L LYS* 1.3 58.9 + - - +
70L GLY 3.4 19.6 + - - -
71L SER 3.4 18.6 + - - -
73L ARG* 3.2 36.6 - - - +
93L ARG* 4.3 6.9 - - - +
97L ILE* 3.6 20.7 - - - +
100L ILE* 4.8 6.4 - - - +
104L ARG* 4.9 1.6 - - - +
125L ARG 3.3 10.3 - - - +
126L HIS* 4.6 1.3 - - - +
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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