Contacts of the strand formed by residues 57 - 65 (chain G) in PDB entry 3CJB
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 LEU 57 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G GLY 3.4 13.0 - - - +
13G LYS 4.5 4.0 - - - +
14G GLU* 4.4 7.4 - - - +
15G PRO* 4.2 17.5 - - + -
49G THR* 3.7 17.0 - - + -
50G VAL 3.5 5.4 - - - +
51G GLN* 3.3 25.6 - - - +
52G LEU* 3.6 8.3 - - - +
55G GLY 4.9 2.5 - - - +
56G ASN* 1.3 86.2 + - - +
58G GLN* 1.3 59.5 + - - +
59G TYR* 3.2 33.9 - - + +
91G ARG* 3.2 27.2 + - - +
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Residues in contact with GLN 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G LYS 3.3 4.9 - - - +
49G THR* 3.3 4.5 - - - +
50G VAL* 2.7 57.2 + - + +
52G LEU* 3.6 26.5 - - + +
57G LEU* 1.3 73.1 - - - +
59G TYR* 1.3 69.0 + - - +
60G ASP* 2.7 30.2 + - - +
93G VAL* 6.1 1.7 - - + +
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Residues in contact with TYR 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G GLY* 2.5 31.8 + - - -
47G LEU* 3.6 20.4 - - + -
48G LYS 3.6 0.9 - - - -
49G THR* 3.6 26.5 - - + -
57G LEU* 3.2 18.0 - - + +
58G GLN* 1.3 81.8 - - - +
60G ASP* 1.3 69.0 + - - +
88G LEU* 3.9 37.2 - - + +
91G ARG* 3.7 37.5 + - + +
92G ALA* 3.5 24.3 - - + +
93G VAL* 3.4 19.8 + - - +
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Residues in contact with ASP 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G ILE 3.6 0.9 - - - +
47G LEU* 3.7 1.2 - - - +
48G LYS* 3.0 36.6 + - + +
50G VAL* 4.9 2.3 - - - +
58G GLN* 2.7 34.3 + - - +
59G TYR* 1.3 79.9 - - - +
61G LEU* 1.3 62.5 + - - +
62G HIS* 3.6 25.2 - - - +
93G VAL* 3.7 13.0 - - - +
95G HIS* 3.6 16.8 + - - +
105G THR* 5.6 3.2 - - - +
109G TYR* 3.8 9.9 + - - +
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Residues in contact with LEU 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G TRP* 5.3 0.2 - - + -
45G VAL* 4.3 16.6 - - + -
46G ILE 3.5 15.0 - - - +
47G LEU* 3.7 26.0 - - + -
59G TYR 4.2 0.4 - - - -
60G ASP* 1.3 71.0 - - - +
62G HIS* 1.3 56.5 + - - +
63G TYR 4.2 0.2 - - - -
81G THR* 3.6 33.0 - - + +
84G LEU* 3.3 36.8 - - + -
85G ASP* 3.8 7.4 - - + +
88G LEU* 5.6 2.0 - - + -
92G ALA* 4.2 18.4 - - + +
93G VAL 2.9 14.9 + - - +
94G GLN* 3.5 1.9 - - + -
95G HIS* 2.7 34.1 + - - +
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Residues in contact with HIS 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45G VAL* 3.7 0.8 - - - -
46G ILE* 2.7 49.0 + - + +
60G ASP* 3.6 17.5 - - - +
61G LEU* 1.3 75.0 - - - +
63G TYR* 1.3 58.9 + - - +
64G TRP 3.9 0.2 - - - -
81G THR* 4.9 1.6 - - - -
95G HIS* 3.2 37.4 + + - +
97G GLU* 3.0 30.0 + - + +
103G SER* 4.5 2.0 - - - -
105G THR* 4.5 9.0 - - + -
106G PHE* 3.8 27.8 - + + -
109G TYR* 2.6 42.3 + + - -
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Residues in contact with TYR 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A GLY 3.5 20.9 - - - -
147A ARG* 3.8 0.3 - - - +
148A THR* 3.3 46.7 + - + -
149A THR 4.8 0.5 + - - -
44G TYR 3.5 11.2 - - - +
45G VAL* 4.4 2.0 - - + +
62G HIS* 1.3 71.7 - - - +
64G TRP* 1.3 61.0 + - - +
65G LEU* 4.0 8.7 + - + +
77G ALA* 4.0 15.3 - - + +
78G ALA* 4.1 16.2 - - + -
81G THR* 3.3 35.4 - - + +
94G GLN* 5.0 0.7 - - + -
95G HIS 2.9 37.5 + - - -
96G ARG* 3.3 32.6 - - + +
97G GLU* 3.0 23.6 + - - +
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Residues in contact with TRP 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G PHE* 3.7 27.8 - + + -
39G PHE 3.6 22.4 - - - -
40G THR* 4.2 1.6 - - - -
42G ASP 3.8 2.7 - - - -
43G ALA* 3.5 8.0 - - - +
44G TYR* 3.0 53.0 + + + +
46G ILE* 4.1 17.7 - - + -
62G HIS 3.9 2.4 + - - -
63G TYR* 1.3 72.3 - - - +
65G LEU* 1.3 61.4 + - - +
66G GLY* 3.6 12.8 - - - -
77G ALA* 5.0 0.2 - - - +
97G GLU* 3.2 22.2 - - + -
99G GLN* 3.3 47.4 - - + +
102G GLU* 3.4 20.2 + - + +
106G PHE* 3.6 27.5 - + + -
114G LEU* 5.1 0.8 - - - +
116G TYR* 3.6 19.0 - + - -
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Residues in contact with LEU 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A SER 5.3 0.2 - - - +
146A GLY* 3.8 7.9 - - - +
43G ALA* 4.4 6.1 - - + -
63G TYR* 4.5 9.0 - - + +
64G TRP* 1.3 81.4 - - - +
66G GLY* 1.3 67.7 - - - +
69G CYS* 4.4 3.8 - - - -
74G SER* 3.6 43.3 - - - +
77G ALA* 4.5 6.3 - - + -
96G ARG* 3.1 48.9 - - + +
97G GLU 2.9 13.7 + - - +
98G VAL* 4.0 11.0 - - + +
99G GLN* 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