Contacts of the strand formed by residues 97 - 102 (chain A) in PDB entry 2JJ6
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 ARG 97 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A GLU* 2.7 68.2 + - + +
96A PRO* 1.3 93.0 - - + +
98A PHE* 1.3 63.3 + - - +
99A ARG* 3.2 30.9 - - - +
109A ASP* 3.8 9.1 + - + -
110A PHE 3.4 14.8 - - - +
111A TYR* 2.9 51.3 + - + -
112A HIS* 3.3 14.9 - - - -
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Residues in contact with PHE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A MET* 4.2 9.4 - - + -
34A LEU* 4.0 20.9 - - + -
47A ALA* 4.5 12.1 - - + -
48A ILE* 4.0 37.0 - - + -
91A ILE* 3.6 26.9 - - + -
92A LEU 3.1 6.5 - - - +
93A CYS* 3.9 29.4 - - + -
97A ARG* 1.3 77.0 - - - +
99A ARG* 1.3 58.7 + - - +
100A VAL* 4.1 2.3 + - + +
109A ASP* 3.3 4.0 - - - -
110A PHE* 2.8 43.1 + + + +
112A HIS* 3.6 26.2 - + - -
117A LEU* 4.9 0.4 - - + -
120A ILE* 4.1 20.6 - - + -
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Residues in contact with ARG 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ILE* 3.8 0.2 - - - -
92A LEU* 2.8 36.0 + - + +
94A GLU* 3.9 25.0 + - - +
97A ARG* 3.2 31.6 + - - +
98A PHE* 1.3 74.5 - - - +
100A VAL* 1.3 61.2 + - - +
101A PHE* 3.6 34.1 - - + -
106A GLN* 3.6 24.1 - - + +
109A ASP* 2.8 39.8 + - - +
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Residues in contact with VAL 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ILE* 4.4 18.4 - - + -
50A LEU* 4.2 16.6 - - + -
89A VAL* 4.3 7.0 - - + -
90A GLU 3.5 8.3 - - - +
91A ILE* 4.5 14.6 - - + -
98A PHE* 4.8 2.7 - - + +
99A ARG* 1.3 79.4 - - - +
101A PHE* 1.3 71.4 + - - +
102A VAL* 4.5 6.1 - - + -
106A GLN* 3.5 3.5 - - - -
107A LEU* 2.9 25.6 + - - +
108A PHE* 2.9 58.0 + - + +
110A PHE* 5.4 0.4 - - + -
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Residues in contact with PHE 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS* 5.6 5.6 - - - -
88A ARG 3.8 0.4 - - - +
89A VAL* 3.5 3.3 - - - -
90A GLU* 2.9 64.5 + - + +
92A LEU* 3.8 24.7 - - + -
99A ARG* 3.6 39.3 - - + -
100A VAL* 1.3 74.2 - - - +
102A VAL* 1.3 66.2 + - - +
104A GLY* 4.4 6.3 - - - -
105A HIS* 3.1 15.9 - - - +
106A GLN* 3.4 33.7 - - + -
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Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 5.0 3.8 - - + -
78A TYR* 5.0 6.2 + - - +
80A PRO* 3.8 24.0 - - + -
81A PHE* 3.8 24.2 - - + -
87A PHE* 5.2 0.4 - - + -
88A ARG 3.2 9.9 - - - +
89A VAL* 4.4 7.6 - - + -
100A VAL* 4.5 10.3 - - + -
101A PHE* 1.3 78.8 - - - +
103A ASP* 1.3 83.8 + - - +
104A GLY 3.1 0.7 + - - -
105A HIS* 2.9 18.7 + - - +
107A LEU* 3.5 34.9 - - + +
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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