Contacts of the strand formed by residues 99 - 104 (chain A) in PDB entry 2JG3
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 PHE 99 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG* 3.2 48.0 - - + +
44A LEU* 3.6 30.5 - - + -
68A VAL* 3.8 26.7 - - + -
93A TRP* 3.6 37.2 - + - -
95A PRO* 4.3 4.0 - - + -
97A GLU 3.6 15.7 - - - -
98A ALA* 1.3 77.6 - - - +
100A ASP* 1.3 62.9 + - - +
102A ILE* 3.9 18.6 - - + -
153A LEU* 2.8 23.7 + - + +
154A LEU* 3.4 7.1 - - - +
155A LYS* 2.9 24.5 + - - +
158A GLY* 4.5 0.5 - - - -
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Residues in contact with ASP 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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36A GLU 4.5 2.6 - - - +
37A ALA* 4.5 3.3 - - + -
38A PRO* 3.7 37.1 - - + +
41A GLY* 3.4 5.0 - - - -
42A ARG 2.9 30.3 + - - +
99A PHE* 1.3 73.5 - - - +
101A LEU* 1.3 60.9 + - - +
154A LEU* 4.4 0.4 - - - -
155A LYS* 2.7 40.9 + - - +
158A GLY* 3.4 7.8 - - - -
159A VAL* 2.9 27.5 + - - +
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Residues in contact with LEU 101 (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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35A ALA* 3.9 18.8 - - + -
36A GLU 3.8 20.0 - - - +
37A ALA* 4.1 7.4 - - + -
42A ARG 3.1 4.9 + - - +
43A VAL* 3.3 17.8 - - + -
44A LEU* 2.7 31.4 + - - +
57A PHE* 3.3 43.3 - - + -
99A PHE* 4.2 0.5 - - - +
100A ASP* 1.3 78.9 - - - +
102A ILE* 1.3 69.1 + - - +
103A LEU* 4.2 11.7 - - + -
159A VAL* 3.2 27.8 - - + +
161A VAL* 4.5 3.1 - - + -
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Residues in contact with ILE 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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44A LEU* 3.3 18.8 - - + +
46A PRO* 3.7 30.7 - - + -
90A PHE* 5.1 0.2 - - + -
99A PHE* 3.9 11.4 - - + -
101A LEU* 1.3 79.1 - - - +
103A LEU* 1.3 63.4 + - - +
150A ALA* 3.2 36.1 - - + +
153A LEU* 3.8 20.4 - - + -
154A LEU* 3.6 18.4 - - + -
159A VAL 3.0 5.5 + - - +
160A LEU* 3.0 11.9 - - + +
161A VAL 2.9 23.4 + - - -
162A PHE* 3.7 15.5 - - + -
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Residues in contact with LEU 103 (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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31A MET* 5.3 2.0 - - + +
32A VAL* 4.3 16.4 - - + +
35A ALA* 4.4 9.9 - - + -
43A VAL* 4.0 20.2 - - + -
44A LEU 2.9 19.4 + - - +
45A GLU* 3.4 30.8 - - + +
46A PRO* 3.4 2.8 - - - +
53A PHE* 4.1 40.4 - - + +
54A LEU* 4.5 3.8 - - + -
57A PHE* 4.4 16.6 - - + -
101A LEU* 4.2 11.2 - - + -
102A ILE* 1.3 77.6 - - - +
104A GLY* 1.3 58.9 + - - +
161A VAL* 3.3 17.9 - - + +
162A PHE* 3.9 7.2 - - - -
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Residues in contact with GLY 104 (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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31A MET* 3.2 5.9 - - - +
45A GLU* 4.5 3.1 - - - -
46A PRO* 5.1 2.0 - - - -
53A PHE* 3.6 27.4 - - - -
103A LEU* 1.3 78.6 - - - +
105A ASN* 1.3 60.1 + - - -
106A PRO* 3.6 4.2 - - - +
161A VAL 3.1 6.7 + - - -
162A PHE* 3.3 9.7 - - - -
163A VAL 3.2 23.2 + - - -
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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