Contacts of the strand formed by residues 126 - 134 (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 HIS 126 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32L ARG* 4.0 26.8 + - + -
66L ALA* 3.9 24.5 - - + -
67L ILE 3.5 10.5 - - - +
68L ARG* 4.6 0.7 - - - +
69L LYS* 3.2 10.3 - - - +
122L GLU* 3.0 20.3 - - - +
123L ASP* 2.7 38.0 + - - +
125L ARG* 1.3 93.9 - - + +
127L LYS* 1.3 62.4 + - - +
128L TRP* 3.7 25.2 - + + -
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Residues in contact with LYS 127 (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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4020 U 4.7 6.7 + - - -
4030 C 2.7 40.6 + - - -
4040 G 5.5 0.9 - - - -
65L VAL 3.6 1.2 - - - +
66L ALA* 3.5 3.8 - - - -
67L ILE* 2.9 34.7 + - - +
69L LYS* 3.6 9.4 - - + +
97L ILE* 3.6 37.3 - - + +
121L GLY 3.8 5.8 - - - +
122L GLU* 3.2 30.3 - - + +
126L HIS* 1.3 75.2 - - - +
128L TRP* 1.3 62.4 + - - +
129L HIS* 4.2 14.8 + - + -
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Residues in contact with TRP 128 (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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28L MET* 3.5 32.1 - - + -
31L TRP* 3.4 43.7 + + + +
32L ARG* 3.9 16.8 - - + -
64L ARG* 3.8 22.7 - - + -
65L VAL 3.4 3.1 - - - -
66L ALA* 3.7 27.9 - - + +
119L SER* 3.8 2.3 + - - -
120L VAL* 2.9 41.3 + - + -
121L GLY 2.9 13.5 + - - +
122L GLU* 3.7 17.5 - - - -
123L ASP* 3.3 37.2 - - - -
126L HIS* 3.7 21.3 - + + -
127L LYS* 1.3 73.2 - - - +
129L HIS* 1.3 66.8 + - - +
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Residues in contact with HIS 129 (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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63L VAL 3.6 0.3 - - - +
64L ARG* 3.3 1.3 - - - -
65L VAL* 2.8 33.6 + - - +
67L ILE* 5.4 0.4 - - - +
97L ILE* 4.0 14.9 - - + +
98L GLN* 3.5 51.1 + - + +
101L ALA* 4.1 21.1 - - + +
117L SER* 5.0 4.3 - - - +
118L TYR 3.2 8.3 - - - +
119L SER* 3.6 32.3 - - - -
120L VAL* 4.1 2.5 - - - -
127L LYS* 4.2 19.2 + - + -
128L TRP* 1.3 80.3 + - - +
130L GLU* 1.3 66.1 + - - +
131L VAL* 3.9 2.5 + - + +
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Residues in contact with GLU 130 (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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40L ILE* 3.4 26.1 - - + +
43L PRO* 3.8 0.2 - - - +
44L THR* 2.7 39.4 + - - -
62L VAL* 4.3 4.4 - - + +
63L VAL 3.2 2.7 - - - +
64L ARG* 3.3 33.5 + - + -
117L SER* 3.3 2.6 - - - -
118L TYR* 2.6 77.2 + - + +
120L VAL* 3.5 14.8 - - + +
129L HIS* 1.3 72.3 - - - +
131L VAL* 1.3 62.0 + - - +
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Residues in contact with VAL 131 (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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62L VAL* 3.3 5.2 - - - -
63L VAL 2.7 38.8 + - - +
65L VAL* 4.2 6.3 - - + -
101L ALA* 4.1 7.4 - - + +
102L GLU* 4.1 15.5 - - + +
105L ALA* 3.9 23.1 - - + -
114L VAL* 3.6 30.5 - - + -
116L ASN 3.7 4.7 - - - +
117L SER* 4.0 11.0 - - - -
129L HIS* 4.4 4.7 - - + +
130L GLU* 1.3 76.4 - - - +
132L ILE* 1.3 64.3 + - - +
133L LEU* 3.4 21.5 - - + +
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Residues in contact with ILE 132 (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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49L ALA* 3.9 33.9 - - + +
52L LEU* 4.0 26.5 - - + -
54L TYR* 4.1 15.9 - - + +
60L ILE* 4.5 10.3 - - + -
61L ILE 3.4 9.6 - - - +
62L VAL* 4.6 10.1 - - + -
114L VAL* 3.7 2.6 - - - +
115L LEU* 2.8 45.7 + - + +
116L ASN* 2.9 20.6 + - + +
118L TYR* 4.4 12.1 - - + -
130L GLU 5.0 0.2 - - - +
131L VAL* 1.3 75.3 - - - +
133L LEU* 1.3 60.8 + - - +
134L ILE* 4.4 8.1 - - + -
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Residues in contact with LEU 133 (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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61L ILE* 2.7 37.0 + - + +
63L VAL* 4.0 22.9 - - + -
105L ALA* 4.1 2.7 - - + +
106L ASN* 4.0 25.4 - - + +
109L PHE* 3.8 23.3 - - + -
112L LEU* 3.8 26.5 - - + -
113L ARG 3.2 9.4 - - - +
114L VAL* 4.5 8.3 - - + -
131L VAL* 3.4 34.1 - - + +
132L ILE* 1.3 74.8 - - - +
134L ILE* 1.3 71.7 + - - +
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Residues in contact with ILE 134 (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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53L GLY 5.7 1.6 - - - +
59L GLY 3.4 1.8 - - - -
60L ILE* 3.7 32.1 - - + -
112L LEU* 3.4 5.9 - - - -
113L ARG* 2.8 26.8 + - - +
115L LEU* 3.8 27.4 - - + -
132L ILE* 4.4 8.1 - - + -
133L LEU* 1.3 87.9 - - - +
135L ASP* 1.3 63.1 + - - +
136L PRO* 2.9 14.7 - - - +
141L ILE* 3.5 32.8 - - + -
147L LEU* 4.8 12.6 - - + -
150L ILE* 3.8 25.8 - - + -
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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