Contacts of the strand formed by residues 42 - 48 (chain S) in PDB entry 5JBA
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 CYS 42 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32S VAL* 3.7 8.7 - - - +
33S LEU* 2.9 34.4 + - + -
40S ALA 3.4 1.2 - - - -
41S PHE* 1.3 101.2 - - + +
43S GLY* 1.3 60.2 + - - +
58S CYS* 2.0 52.9 - - + -
141S TRP* 6.4 0.2 - - - -
193S GLY 3.4 12.6 - - - -
195S SER* 3.2 12.6 - - - +
302S 0G6 4.2 6.3 - - - -
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Residues in contact with GLY 43 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30S GLN* 3.8 11.0 - - - -
31S VAL 3.3 12.6 - - - -
32S VAL* 4.5 0.9 - - - -
33S LEU* 3.9 7.4 - - - +
42S CYS* 1.3 75.2 - - - +
44S GLY* 1.3 53.3 + - - -
54S THR* 2.7 28.1 + - - -
141S TRP* 5.8 1.3 - - - -
193S GLY 4.0 3.2 + - - -
194S ASP* 4.2 2.6 + - - -
195S SER 2.8 11.0 + - - +
196S GLY* 3.3 10.4 - - - -
197S GLY* 3.9 4.5 - - - -
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Residues in contact with GLY 44 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30S GLN* 3.6 9.0 + - - -
31S VAL* 2.9 39.3 + - - +
33S LEU* 5.3 0.2 - - - -
43S GLY* 1.3 73.6 - - - -
45S SER* 1.3 64.7 + - - -
52S ILE* 3.9 5.6 - - - -
53S VAL 3.3 8.1 - - - -
54S THR* 4.3 0.9 - - - -
196S GLY 3.2 12.7 + - - -
197S GLY* 3.9 1.0 - - - -
198S PRO* 3.9 1.9 - - - +
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Residues in contact with SER 45 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29S TRP* 3.2 8.5 - - - -
31S VAL* 5.0 0.2 - - - -
44S GLY* 1.3 71.6 - - - -
46S ILE* 1.3 63.5 + - - +
47S VAL 3.3 0.5 + - - -
52S ILE* 3.3 7.4 - - - +
53S VAL* 2.9 48.1 + - - +
121S ILE* 3.9 20.0 - - - -
196S GLY 4.7 0.2 + - - -
197S GLY 4.4 0.5 - - - -
198S PRO* 3.1 39.3 - - - +
209S LEU* 4.1 3.7 - - - +
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Residues in contact with ILE 46 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28S PRO 3.6 23.8 - - - +
29S TRP* 2.9 18.2 + - - +
30S GLN 5.2 0.2 - - - +
31S VAL* 3.6 20.6 - - + -
45S SER* 1.3 70.7 - - - +
47S VAL* 1.3 58.4 + - - +
48S ASN 3.3 30.5 - - - +
51S TRP 3.9 3.4 - - - -
52S ILE* 3.9 2.7 - - + -
68S ALA* 4.2 3.6 - - + -
112S LEU* 3.9 15.9 - - + -
114S LEU* 5.0 2.7 - - + -
118S VAL* 3.8 25.8 - - + -
119S THR 3.8 6.1 - - - +
120S PRO* 3.3 21.5 - - + +
121S ILE* 2.9 33.7 + - - +
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Residues in contact with VAL 47 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45S SER 3.3 0.2 + - - -
46S ILE* 1.3 73.0 - - - +
48S ASN* 1.3 66.3 + - - +
51S TRP* 2.8 16.9 + - + +
52S ILE 4.2 1.8 - - - -
53S VAL* 3.8 40.4 - - + +
105S LEU* 4.6 4.7 - - + -
120S PRO* 3.5 15.2 - - - +
121S ILE 4.5 6.3 - - - +
123S ILE* 4.3 13.0 - - + -
238S ILE* 4.1 20.0 - - + -
239S LYS* 6.4 1.3 - - + -
242S THR* 3.7 26.5 - - - +
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Residues in contact with ASN 48 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46S ILE* 3.3 17.4 - - - +
47S VAL* 1.3 80.7 - - - +
49S GLU* 1.3 78.7 + - - +
50S LYS* 2.9 17.2 + - - +
51S TRP* 3.1 30.0 + - - +
112S LEU* 4.5 2.4 - - - +
120S PRO* 4.3 7.9 - - + -
242S THR* 2.9 35.4 + - - -
244S LEU* 3.6 19.6 - - + +
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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