Contacts of the strand formed by residues 107 - 120 (chain A) in PDB entry 3CJE
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 VAL 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A LYS* 3.6 5.9 - - - +
104A ALA* 2.7 40.3 + - + +
105A GLY 3.8 1.7 - - - +
106A PRO* 1.3 95.4 - - + +
108A TYR* 1.3 71.4 + - + +
109A GLU* 5.7 1.3 - - + +
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Residues in contact with TYR 108 (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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101A TRP* 4.0 24.0 - + + -
102A ALA 3.3 13.9 - - - +
103A LYS* 4.6 1.1 - - - -
104A ALA* 4.0 1.1 - - - +
107A VAL* 1.3 87.8 - - + +
109A GLU* 1.3 68.7 + - - +
110A THR* 3.5 30.5 - - + -
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Residues in contact with GLU 109 (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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101A TRP* 3.2 4.5 - - - +
102A ALA* 2.9 36.0 + - + +
104A ALA* 3.5 24.4 - - + +
107A VAL* 5.7 1.7 - - + +
108A TYR* 1.3 79.0 - - - +
110A THR* 1.3 65.4 + - - +
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Residues in contact with THR 110 (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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99A TRP* 5.8 6.3 - - - -
100A ASP* 3.2 9.6 - - - -
101A TRP* 4.1 8.5 - - + -
108A TYR* 3.5 31.0 - - + +
109A GLU* 1.3 83.0 - - - +
111A GLY* 1.3 59.2 + - - +
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Residues in contact with GLY 111 (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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99A TRP* 3.3 10.4 - - - +
100A ASP* 2.9 38.9 + - - +
110A THR* 1.3 78.3 - - - +
112A PRO* 1.3 73.5 - - - +
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Residues in contact with PRO 112 (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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98A VAL 4.0 0.2 - - - +
99A TRP* 3.7 18.8 - - + +
100A ASP* 4.9 2.8 - - - +
111A GLY* 1.3 86.6 - - - +
113A LYS* 1.3 60.3 + - - +
115A PHE* 4.2 24.0 - - + -
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Residues in contact with LYS 113 (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 ARG* 3.3 28.7 - - - +
13A GLU* 2.6 32.3 + - + +
98A VAL* 2.8 32.0 + - + +
99A TRP* 4.4 2.0 - - - -
100A ASP* 4.0 21.2 + - - +
111A GLY 3.8 0.2 + - - -
112A PRO* 1.3 74.2 - - - +
114A SER* 1.3 63.5 + - - +
115A PHE* 5.6 0.4 - - - -
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Residues in contact with SER 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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96A ARG* 4.4 7.9 + - - -
97A VAL* 3.4 5.0 - - - +
98A VAL* 3.0 51.4 + - - +
113A LYS* 1.3 82.6 - - - +
115A PHE* 1.3 73.2 + - - +
116A GLU* 4.8 9.6 + - - -
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Residues in contact with PHE 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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65A PHE* 4.0 13.7 - + - -
69A LEU* 4.0 12.1 - - + -
95A CYS* 5.6 0.4 - - - -
96A ARG 3.6 2.7 - - - -
97A VAL* 3.6 38.4 - - + -
99A TRP* 5.1 4.0 - - - -
112A PRO* 4.2 24.5 - - + -
113A LYS 5.6 0.2 - - - -
114A SER* 1.3 80.6 - - - +
116A GLU* 1.3 67.0 + - - +
117A ILE* 5.9 3.8 - - + -
147A LEU* 4.0 37.5 - - + -
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Residues in contact with GLU 116 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A GLU 3.9 0.6 - - - +
95A CYS* 3.2 6.0 - - - -
96A ARG* 2.9 74.6 + - + +
114A SER* 4.8 9.9 + - - +
115A PHE* 1.3 81.0 - - - +
117A ILE* 1.3 64.1 + - - +
118A ASP* 4.2 7.0 - - - +
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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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69A LEU* 4.4 20.4 - - + -
70A THR* 6.1 1.1 - - - -
73A VAL* 3.9 17.7 - - + -
93A VAL* 3.6 27.4 - - + -
94A GLU 3.4 2.7 - - - +
95A CYS* 4.1 13.2 - - + -
115A PHE* 5.5 3.8 - - + -
116A GLU* 1.3 80.1 - - - +
118A ASP* 1.3 66.9 + - - +
119A ILE* 4.0 22.0 + - + +
144A GLU* 3.5 27.1 - - - +
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Residues in contact with ASP 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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92A ASP 4.0 0.9 - - - +
93A VAL* 3.4 4.0 - - - +
94A GLU* 2.8 59.3 + - + +
116A GLU* 4.2 6.5 - - - +
117A ILE* 1.3 79.6 + - - +
119A ILE* 1.3 61.8 + - - +
120A ILE* 5.1 2.2 - - + +
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Residues in contact with ILE 119 (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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73A VAL* 4.6 5.6 - - + -
77A ILE* 4.1 17.9 - - + -
91A LEU* 4.3 4.0 - - + -
92A ASP 3.8 2.2 - - - -
93A VAL* 4.3 9.9 - - + -
117A ILE* 4.0 25.8 + - + +
118A ASP* 1.3 80.2 - - - +
120A ILE* 1.3 66.5 + - - +
121A LEU* 3.5 34.1 + - + +
134A ILE* 3.8 43.6 - - + +
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Residues in contact with ILE 120 (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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90A ASP 4.2 0.9 - - - +
91A LEU* 3.5 8.1 - - - +
92A ASP* 2.8 53.2 + - + +
94A GLU* 4.1 21.3 - - - +
118A ASP* 5.1 2.0 - - + +
119A ILE* 1.3 78.1 - - - +
121A LEU* 1.3 62.7 - - - +
122A HIS* 3.4 35.9 - - + +
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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