Contacts of the strand formed by residues 34 - 41 (chain K) in PDB entry 3Q3G
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 ILE 34 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29K PHE* 4.0 24.9 - - + -
30K ASN 4.0 4.7 - - - +
31K ILE* 3.3 16.2 + - - +
32K LYS 4.2 2.8 - - - +
33K ASP* 1.3 83.7 - - + +
35K TYR* 1.4 76.9 + - - +
36K MET* 3.6 35.9 - - + +
54K ASP* 4.3 1.7 - - - +
55K PRO* 3.3 20.5 - - + +
100K SER* 3.8 19.1 - - - +
101K GLU 3.7 5.8 - - - +
102K GLY* 3.8 21.1 - - - -
103K HIS* 3.7 15.4 - - - -
104K TYR* 5.6 1.6 - - - +
113K TYR* 6.2 0.7 - - + -
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Residues in contact with TYR 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100J TYR* 4.4 1.1 - - - -
34K ILE* 1.4 78.1 - - - +
36K MET* 1.3 61.9 + - - +
37K GLN* 3.5 16.4 + - - +
52K ARG* 3.9 20.6 + - - -
53K ILE 3.4 3.4 - - - -
54K ASP* 3.6 39.0 + - + -
100K SER* 3.4 4.3 - - - -
101K GLU* 2.9 58.6 + - + +
103K HIS* 3.5 26.0 - + - -
177L SER* 4.7 0.2 + - - -
178L GLU* 3.4 38.8 - - - +
179L GLU* 4.9 2.6 - - - +
205L LEU* 4.0 3.2 + - - +
206L LEU 3.2 24.6 + - - -
207L GLY* 4.2 5.4 - - - -
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Residues in contact with MET 36 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K LEU* 4.1 14.8 - - + -
24K CYS* 4.0 17.5 - - - +
26K PRO* 3.8 17.5 - - + -
31K ILE* 3.6 30.7 - - + -
34K ILE* 3.6 17.7 + - + +
35K TYR* 1.3 70.8 - - - +
37K GLN* 1.3 66.1 + - - +
38K TRP* 4.5 5.7 - - - +
52K ARG* 3.2 4.8 - - - -
53K ILE* 2.9 52.0 + - + +
55K PRO* 4.6 3.8 - - + +
81K ALA* 3.7 24.2 - - + -
98K CYS* 4.6 6.1 - - + -
99K ALA 3.8 13.5 - - - +
100K SER* 4.3 0.4 - - - -
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Residues in contact with GLN 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100J TYR* 5.4 0.2 + - - -
102J LEU* 3.4 14.7 - - - +
35K TYR* 3.5 29.6 + - - +
36K MET* 1.3 75.1 - - - +
38K TRP* 1.3 66.6 + - - +
39K VAL* 4.3 1.6 - - + -
49K TRP* 2.8 32.7 + - + +
51K GLY 3.6 4.5 - - - -
52K ARG* 3.4 22.5 - - - +
98K CYS* 3.3 8.7 - - - +
99K ALA* 2.7 40.6 + - + +
101K GLU* 3.7 16.7 + - - +
111K MET* 3.8 33.7 - - + -
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Residues in contact with TRP 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K GLN* 3.8 21.1 - - - -
22K LEU* 4.1 20.9 - - + -
23K SER 4.1 7.4 - - - -
24K CYS* 3.8 30.5 - - + -
36K MET* 4.5 3.9 - - - +
37K GLN* 1.3 81.5 + - - +
39K VAL* 1.4 58.1 + - - +
49K TRP* 3.9 1.6 - - - -
50K ILE* 2.8 47.9 + - + +
51K GLY 3.0 11.8 + - - +
72K ILE* 3.6 34.6 - - + +
81K ALA* 3.8 18.2 - - - +
82K TYR 3.5 14.9 + - - +
83K LEU* 3.5 37.0 - - + -
96K TYR* 4.5 8.7 - - + -
97K TYR 3.4 19.3 - - - -
98K CYS* 3.9 7.0 - - + -
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Residues in contact with VAL 39 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104J PHE* 4.3 6.7 - - + -
37K GLN* 4.7 1.6 - - + -
38K TRP* 1.4 79.8 - - - +
40K LYS* 1.3 62.2 + - - +
47K LEU* 3.8 27.8 - - + -
48K GLU 3.5 26.2 - - - +
49K TRP* 4.4 7.6 - - + -
50K ILE* 4.4 3.6 - - - +
95K VAL 3.9 0.5 - - - +
96K TYR* 3.5 2.3 - - - -
97K TYR* 2.8 41.4 + - + +
99K ALA* 5.0 1.1 - - + -
111K MET* 4.1 22.9 - - + -
114K TRP* 4.0 28.3 - - + -
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Residues in contact with LYS 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K VAL* 1.3 73.1 - - - +
41K GLN* 1.4 62.2 + - - +
42K ARG* 3.7 21.1 + - + +
46K GLY 3.6 2.1 - - - +
48K GLU* 2.7 65.1 + - + +
50K ILE* 3.9 9.3 - - + +
66K PHE* 3.9 22.3 - - + -
91K GLU* 2.8 32.6 + - - +
92K ASP* 3.9 11.7 + - - +
94K ALA* 3.7 10.1 - - + -
95K VAL 3.8 3.4 - - - -
96K TYR* 3.6 34.5 + - + +
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Residues in contact with GLN 41 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44J GLN* 2.8 44.5 + - - +
93J TYR* 3.5 13.3 + - - -
40K LYS* 1.4 72.6 - - - +
42K ARG* 1.3 70.5 + - - +
43K PRO 3.9 0.3 - - - -
45K GLN 3.7 10.6 - - - +
46K GLY 3.8 5.3 - - - +
47K LEU* 3.5 17.4 - - + +
94K ALA* 3.7 3.3 - - - -
95K VAL* 2.8 44.1 + - + +
97K TYR* 3.3 25.9 + - + -
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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