Contacts of the strand formed by residues 113 - 118 (chain A) in PDB entry 1PJJ
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 THR 113 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A MET* 3.5 7.9 - - - +
34A LEU* 3.9 35.2 - - + -
70A ILE 3.7 1.1 + - - +
71A SER* 3.3 1.7 - - - -
72A HIS* 3.0 35.5 + - - +
74A ARG* 4.6 7.2 - - - +
111A PHE 3.4 10.8 - - - +
112A GLY* 1.3 80.6 - - - +
114A TRP* 1.3 72.3 + - - +
115A GLU* 4.6 1.4 + - - -
1004A GOL 3.0 32.7 + - - +
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Residues in contact with TRP 114 (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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25A ILE* 4.7 9.4 - - + -
32A MET* 3.0 21.9 + - + +
33A VAL* 3.3 18.2 - - + +
34A LEU 2.8 26.5 + - - -
37A PHE* 5.9 0.4 - + - -
40A LEU* 3.8 31.9 - - + -
61A PHE* 5.4 1.3 - + - -
69A LEU* 3.9 24.7 - - + -
70A ILE 3.4 3.1 - - - -
71A SER* 3.7 13.8 + - - -
79A TYR* 2.9 37.1 + + - -
94A LEU* 3.5 40.9 - - + +
95A THR 5.4 1.8 - - - -
96A MET* 3.9 28.3 - - + -
103A LEU* 6.0 2.0 - - + -
105A TYR* 4.6 5.9 - + + -
113A THR* 1.3 85.7 - - - +
115A GLU* 1.3 64.0 + - - +
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Residues in contact with GLU 115 (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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34A LEU* 3.7 29.6 - - + +
35A THR* 3.7 14.2 - - + +
68A ARG 3.5 2.8 - - - +
69A LEU* 3.6 4.5 - - - +
70A ILE* 2.8 47.8 + - + +
113A THR* 4.6 2.8 + - - -
114A TRP* 1.3 80.9 - - - +
116A LEU* 1.3 60.9 + - - +
117A ILE* 3.8 8.3 + - + +
125A TYR* 2.6 25.4 + - + -
129A LYS* 5.1 1.7 + - - -
1004A GOL 2.4 31.1 + - - -
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Residues in contact with LEU 116 (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 THR* 2.9 28.6 + - - +
39A GLN 5.0 0.7 - - - -
40A LEU* 3.8 39.2 - - + +
43A GLU* 3.9 23.3 - - + -
44A LEU* 4.1 22.4 - - + -
67A PHE* 4.0 33.0 - - + -
68A ARG 3.7 16.6 - - - +
69A LEU* 4.4 2.7 - - - +
115A GLU* 1.3 70.5 - - - +
117A ILE* 1.3 68.5 + - - +
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Residues in contact with ILE 117 (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 THR* 4.9 4.7 - - + -
67A PHE* 3.8 4.8 - - - -
68A ARG* 2.8 45.2 + - + +
70A ILE* 3.4 29.2 - - + -
115A GLU* 4.6 10.8 - - + +
116A LEU* 1.3 85.7 - - - +
118A SER* 1.3 62.0 + - - +
121A GLN* 3.6 42.6 - - + +
122A VAL* 3.8 7.9 - - + -
125A TYR* 4.0 15.5 - - + -
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Residues in contact with SER 118 (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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66A ASP* 3.2 15.3 - - - -
67A PHE* 5.3 2.5 - - - -
68A ARG* 4.3 1.1 - - - -
117A ILE* 1.3 75.3 - - - +
119A THR* 1.3 66.9 + - - +
120A ASP* 3.0 14.2 + - - -
121A GLN* 2.8 54.4 + - - +
122A VAL* 3.5 7.4 + - - +
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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