Contacts of the strand formed by residues 47 - 53 (chain h) in PDB entry 5GJQ
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 47 (chain h).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43h ARG 3.7 0.2 - - - -
44h GLY* 2.7 33.0 + - - -
45h LYS 3.8 0.4 - - - -
46h ASP* 1.3 93.0 - - - +
48h ALA* 1.3 59.7 + - - +
49h VAL* 4.5 1.6 - - - -
143h ILE* 4.7 0.7 - - - -
149h PRO* 3.3 19.2 - - - +
191h PHE* 4.0 26.0 - - + -
194h THR* 3.5 31.9 - - - -
220h VAL 3.4 13.5 - - - +
221h THR* 3.9 12.3 - - + +
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Residues in contact with ALA 48 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42h VAL 3.5 8.3 - - - +
43h ARG* 4.9 0.7 - - - -
44h GLY 4.4 0.2 - - - +
47h CYS* 1.3 77.6 - - - +
49h VAL* 1.3 64.0 + - - +
141h ILE* 3.9 18.9 - - + +
149h PRO* 4.5 7.9 - - + -
150h GLN 4.2 11.4 - - - +
151h VAL* 4.3 5.6 - - + -
219h VAL* 3.2 6.1 - - - +
220h VAL* 2.9 47.8 + - + +
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Residues in contact with VAL 49 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40h VAL 3.9 0.6 - - - +
41h ALA* 3.3 5.4 - - - +
42h VAL 2.8 35.6 + - - +
47h CYS* 4.5 5.4 - - - -
48h ALA* 1.3 82.6 - - - +
50h ILE* 1.3 75.5 + - - +
51h VAL* 5.4 0.7 - - + -
141h ILE* 4.9 1.3 - - - +
191h PHE* 4.7 0.2 - - + -
194h THR* 3.6 27.1 - - + +
195h VAL* 3.9 28.5 - - + +
198h ALA* 4.6 10.7 - - + +
217h VAL* 3.8 14.1 - - + -
218h GLY 3.6 9.9 - - - +
219h VAL* 3.7 13.7 - - + -
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Residues in contact with ILE 50 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40h VAL 3.5 4.5 - - - +
41h ALA* 3.5 25.1 - - + -
49h VAL* 1.3 73.5 - - - +
51h VAL* 1.3 66.3 + - - +
52h THR* 4.2 2.2 - - - +
69h LEU* 3.5 29.4 - - + -
78h CYS 5.6 1.1 - - - -
79h VAL* 3.7 23.6 - - + +
139h ILE* 3.9 12.8 - - + +
141h ILE* 3.4 45.5 - - + -
217h VAL* 3.2 9.7 - - - +
218h GLY* 2.8 37.4 + - - +
227h PHE* 5.3 1.3 - - + -
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Residues in contact with VAL 51 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38h THR 4.2 0.3 - - - +
39h SER* 3.4 1.2 - - - -
40h VAL* 2.9 59.8 + - + +
50h ILE* 1.3 76.4 - - - +
52h THR* 1.3 68.9 + - - +
198h ALA* 3.7 28.5 - - + +
199h ILE* 4.5 9.2 - - + -
202h LEU* 4.2 15.3 - - + +
215h ILE* 3.9 19.7 - - + -
216h GLU 3.3 10.5 - - - +
217h VAL* 3.9 17.9 - - + -
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Residues in contact with THR 52 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37h LEU* 4.9 5.2 - - + -
38h THR 3.7 11.9 - - - +
39h SER* 3.0 29.9 + - - +
50h ILE* 4.2 1.9 - - - +
51h VAL* 1.3 81.9 + - - +
53h GLN* 1.3 78.7 + - + +
68h HIS* 4.4 19.1 - - + -
69h LEU* 5.2 2.5 - - - -
79h VAL* 3.3 14.4 - - - +
80h MET 5.7 0.2 - - - +
202h LEU* 4.1 5.8 - - - -
215h ILE* 3.2 2.6 - - - -
216h GLU* 2.9 44.0 + - - +
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Residues in contact with GLN 53 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36h GLY 4.2 2.6 + - - -
37h LEU* 3.4 25.7 - - + +
38h THR* 2.7 50.4 + - - +
52h THR* 1.3 87.7 - - + +
54h LYS* 1.3 59.7 + - - +
55h LYS* 3.0 34.5 + - + +
68h HIS* 4.5 2.6 - - - -
170h VAL* 5.7 0.2 - - - +
202h LEU* 3.8 5.8 - - + +
206h LEU* 3.5 35.3 - - + +
210h PHE* 5.3 3.1 - - + -
214h GLU 3.4 7.6 - - - +
215h ILE* 4.4 3.4 - - - -
216h GLU* 4.4 5.0 - - - +
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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