Contacts of the strand formed by residues 117 - 125 (chain H) 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 LYS 117 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94H ARG* 3.3 2.5 - - - -
95H GLU 3.1 24.5 + - - +
97H LYS* 3.5 51.6 - - + +
116H GLY* 1.3 74.7 - - - -
118H PRO* 1.4 79.3 - - + +
119H VAL* 3.3 2.5 + - + +
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Residues in contact with PRO 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H TYR* 5.0 7.2 - - + +
20H ILE* 4.1 17.3 - - + -
21H SER 3.8 17.5 - - - +
22H GLY 3.8 23.8 - - - +
23H ILE* 4.7 1.1 - - - -
24H PRO* 4.6 8.2 - - + +
92H VAL* 4.4 15.3 - - + -
93H ILE 3.7 8.1 - - - +
94H ARG* 4.5 2.0 - - + -
115H PHE* 6.3 0.7 - - + -
116H GLY 4.2 4.0 - - - +
117H LYS* 1.4 91.8 - - + +
119H VAL* 1.3 62.7 + - - +
120H GLY 3.8 0.4 - - - -
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Residues in contact with VAL 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H TYR* 3.6 17.9 - - + +
24H PRO* 3.7 14.3 - - - +
58H HIS* 5.4 1.7 - - - -
93H ILE* 2.9 18.9 + - + +
94H ARG 3.6 16.4 - - - -
95H GLU* 3.7 18.6 - - + +
97H LYS* 3.8 27.4 - - + +
117H LYS* 3.5 14.6 - - + +
118H PRO* 1.3 75.3 - - - +
120H GLY* 1.3 59.7 + - - +
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Residues in contact with GLY 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H PRO* 3.8 17.1 - - - +
58H HIS* 4.5 8.3 - - - -
92H VAL* 3.5 5.9 - - - +
93H ILE* 2.8 35.6 + - - +
118H PRO 3.8 1.2 - - - -
119H VAL* 1.3 81.3 - - - +
121H THR* 1.3 70.5 + - - +
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Residues in contact with THR 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H ARG* 4.2 9.2 - - - +
23H ILE* 3.6 26.5 - - + -
24H PRO 4.4 8.0 + - - +
26H LYS* 4.9 3.5 - - - +
57H ARG* 3.5 3.3 - - - +
58H HIS* 3.0 46.5 + - - +
89H PRO* 3.6 27.2 - - - +
91H HIS 3.2 9.9 - - - +
92H VAL* 4.5 5.2 - - + -
93H ILE* 3.6 6.3 - - - +
120H GLY* 1.3 80.8 - - - +
122H ALA* 1.3 61.7 + - - +
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Residues in contact with ALA 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H TYR 5.6 0.4 - - - +
55H GLN* 4.3 14.1 - - + +
56H ILE 3.2 24.5 - - - +
57H ARG* 3.7 6.3 - - + +
89H PRO* 3.4 7.6 - - - -
90H PHE 3.1 4.0 + - - -
91H HIS* 2.7 39.3 + - + +
93H ILE* 4.0 18.4 - - + -
121H THR* 1.3 77.3 - - - +
123H ALA* 1.3 59.5 - - - +
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Residues in contact with ALA 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55H GLN* 3.4 2.2 - - - -
56H ILE* 2.8 41.6 + - + +
61H LEU* 4.4 10.8 - - + -
87H LYS* 4.3 18.2 - - + -
88H PHE 3.4 27.6 - - - +
89H PRO* 3.7 4.5 - - + +
90H PHE 4.4 0.2 - - - +
122H ALA* 1.3 74.5 - - - +
124H ARG* 1.3 62.9 + - - +
125H VAL* 3.6 7.0 + - + +
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Residues in contact with ARG 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10040 C 4.3 13.9 + - - -
10050 A 5.8 2.5 + - - -
9H SER* 3.8 28.6 + - - +
11H LYS* 2.5 38.0 + - - +
13H ALA* 3.8 22.6 - - - +
54H VAL 3.6 4.0 - - - +
55H GLN* 2.6 30.2 - - + +
87H LYS* 4.7 4.5 + - - +
91H HIS* 3.4 35.2 + - + +
122H ALA 4.2 0.4 + - - -
123H ALA* 1.3 72.8 - - - +
125H VAL* 1.3 62.0 + - - +
126H HIS* 4.3 14.4 + - + +
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Residues in contact with VAL 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50H VAL* 3.7 34.8 - - + -
52H LYS 3.8 0.9 - - - +
53H PRO* 3.0 3.5 - - - +
54H VAL* 2.9 35.0 + - + +
56H ILE* 4.1 21.8 - - + -
87H LYS* 4.2 26.5 - - + +
123H ALA* 4.0 12.3 - - + +
124H ARG* 1.3 78.5 - - - +
126H HIS* 1.3 69.2 + - - +
129H ASN* 4.1 16.6 - - + +
131H ILE* 4.9 8.1 - - + +
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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