Contacts of the strand formed by residues 26 - 33 (chain H) in PDB entry 2QC8
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 26 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H GLU 3.9 7.6 - - - +
25H LYS* 1.3 82.0 - - - +
27H GLN* 1.3 74.9 + - - +
45H ARG 3.6 0.3 - - - +
46H THR* 3.3 5.6 - - - -
47H LEU* 2.6 44.3 + - + +
49H SER 3.7 7.6 - - - +
50H GLU* 3.5 24.2 - - + +
51H PRO* 4.2 16.6 - - + -
93H PRO* 3.3 43.3 - - + +
94H ASN* 3.9 2.9 - - - +
95H LYS* 4.8 2.0 - - + +
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Residues in contact with GLN 27 (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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18H MET* 5.6 0.2 - - - +
22H GLN* 4.2 1.8 + - - +
26H VAL* 1.3 75.5 - - - +
28H ALA* 1.3 60.3 - - - +
29H MET 4.1 0.2 - - - -
44H THR* 3.8 3.1 - - + -
45H ARG 3.5 5.2 - - - -
46H THR* 5.5 0.4 - - - +
90H ARG* 3.5 41.6 + - - +
94H ASN* 2.7 34.7 + - + +
95H LYS 2.9 25.5 + - - +
177I GLU* 4.8 2.6 + - - -
180I TYR* 3.3 54.2 - - + +
181I ARG* 3.8 17.5 + - - +
184I LEU* 4.3 11.9 - - + -
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Residues in contact with ALA 28 (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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26H VAL 3.9 0.2 + - - -
27H GLN* 1.3 73.9 - - - +
29H MET* 1.3 62.5 + - - +
30H TYR* 3.5 25.3 + - + -
44H THR* 3.3 4.1 - - - +
45H ARG* 2.9 34.6 + - + +
47H LEU* 4.1 24.7 - - + -
57H LEU* 4.2 8.5 - - + -
95H LYS* 3.4 10.3 - - + +
97H VAL* 4.6 4.9 - - + -
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Residues in contact with MET 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H GLN 4.1 0.6 - - - -
28H ALA* 1.3 70.5 - - - +
30H TYR* 1.3 61.8 + - - +
31H ILE* 3.7 6.2 + - + +
42H CYS* 3.4 36.8 - - + -
43H LYS 3.5 7.2 - - - +
44H THR* 3.2 24.6 - - - +
87H ASP* 5.6 0.7 - - - +
89H PHE* 6.0 1.1 - - - -
90H ARG* 3.5 26.0 - - - +
95H LYS 2.8 14.4 + - - +
96H LEU* 3.6 15.7 - - + -
97H VAL 2.9 24.4 + - - +
223H PHE* 3.5 20.6 - - - -
227H ARG* 5.5 7.6 - - - +
173I ARG* 4.4 8.3 - - - +
177I GLU* 4.4 5.4 - - - +
709I CL 3.7 11.9 - - + -
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Residues in contact with TYR 30 (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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28H ALA* 3.7 25.8 - - + -
29H MET* 1.3 73.6 - - - +
31H ILE* 1.3 58.7 + - - +
32H TRP* 3.6 4.1 - - + -
42H CYS* 3.0 25.8 - - - +
43H LYS 2.8 18.1 + - - +
45H ARG* 3.8 20.9 + - - -
57H LEU* 3.9 6.9 - - + +
58H PRO* 2.5 51.5 + - - +
60H TRP* 3.6 35.7 - + + -
79H LEU* 4.3 13.9 - - + -
81H PRO* 4.1 14.6 - - + -
97H VAL* 3.4 14.8 - - + -
99H CYS* 3.7 21.5 - - - -
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Residues in contact with ILE 31 (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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29H MET* 3.9 7.9 - - + +
30H TYR* 1.3 78.3 - - - +
32H TRP* 1.3 67.7 + - - +
40H LEU* 3.8 18.8 - - + -
41H ARG 3.3 9.4 - - - +
42H CYS* 4.0 2.2 - - + -
96H LEU* 3.9 27.6 - - + -
97H VAL 2.7 17.9 + - - +
98H LEU* 3.7 13.8 - - + +
99H CYS* 2.9 29.3 + - - +
219H TRP 5.9 0.4 - - - +
220H VAL* 4.9 9.0 - - + -
223H PHE* 3.6 58.1 - - + -
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Residues in contact with TRP 32 (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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30H TYR* 3.6 8.1 - - + -
31H ILE* 1.3 82.4 - - - +
33H ILE* 1.3 78.2 + - - +
40H LEU* 3.3 8.3 - - - +
41H ARG* 2.8 62.5 + - + +
42H CYS* 3.5 18.8 - - - -
43H LYS* 3.9 11.9 - - + -
62H PHE* 3.3 58.5 - + + -
67H THR* 4.5 0.8 - - - +
69H GLN* 4.3 3.8 - - - +
79H LEU* 3.7 36.6 - - + -
98H LEU* 5.2 2.0 - - - -
99H CYS 4.5 8.7 - - - +
101H VAL* 3.8 11.2 - - + -
162I TYR* 4.5 2.7 - + - -
163I CYS* 3.8 30.5 - - + -
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Residues in contact with ILE 33 (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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32H TRP* 1.3 84.1 - - - +
34H ASP* 1.3 72.1 + - - +
37H GLY* 3.9 28.5 - - - +
38H GLU 4.5 0.2 - - - +
39H GLY 3.4 6.7 - - - +
40H LEU* 4.1 15.5 - - + -
69H GLN* 3.4 10.2 - - - +
98H LEU* 5.2 7.2 - - + -
99H CYS 5.1 5.7 + - - +
101H VAL* 4.0 8.2 - - + +
111H THR* 4.0 20.3 + - - +
112H ASN* 6.2 1.6 - - - -
113H LEU 6.3 0.4 - - - +
219H TRP* 3.7 43.1 - - + +
347H ASP* 4.7 4.9 - - - +
349H PHE* 4.5 11.0 - - + -
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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