Contacts of the strand formed by residues 11 - 19 (chain C) in PDB entry 4UQJ
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 SER 11 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ASN* 1.3 72.4 - - - +
12C ILE* 1.3 61.7 + - - +
13C GLN* 3.7 4.0 + - - +
42C ARG* 3.7 5.2 - - - -
44C THR* 3.2 22.0 + - - -
71C TYR* 4.4 9.7 + - - -
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Residues in contact with ILE 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ASN* 4.9 2.2 - - + +
11C SER* 1.3 75.2 + - - +
13C GLN* 1.3 61.7 + - - +
14C ILE* 3.6 14.8 + - + +
41C PHE* 3.9 27.1 - - + -
42C ARG 3.0 12.7 + - - +
43C LEU* 3.5 11.0 - - + -
44C THR* 2.9 23.8 + - - -
71C TYR* 3.7 31.6 - - + -
296C PHE* 3.6 33.4 - - + +
306C ILE* 6.3 2.7 - - + -
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Residues in contact with GLN 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C SER* 3.7 4.4 + - - +
12C ILE* 1.3 72.4 - - - +
14C ILE* 1.3 60.9 + - - +
44C THR* 3.5 17.5 - - + +
46C HIS* 6.6 0.2 - - + -
68C ARG 5.4 3.1 - - - +
69C GLY 4.3 15.5 - - - +
70C VAL* 3.4 7.2 - - + -
71C TYR* 3.0 38.2 + - + -
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Residues in contact with ILE 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ILE* 3.6 18.6 + - + +
13C GLN* 1.3 80.9 - - - +
15C GLY* 1.3 64.4 + - - +
29C PHE* 4.6 18.2 - - + -
33C MET* 5.1 2.0 - - - -
43C LEU* 4.1 26.2 - - + -
44C THR 3.0 11.8 + - - +
45C PRO* 3.9 11.0 - - + -
46C HIS* 3.0 28.6 + - - +
70C VAL* 3.8 7.1 - - - +
71C TYR* 5.2 0.2 - - + -
72C ALA* 3.3 22.0 - - + +
74C PHE* 5.8 0.4 - - + -
292C MET* 3.7 33.2 - - + -
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Residues in contact with GLY 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ILE* 1.3 78.9 - - - +
16C GLY* 1.3 58.8 + - - -
17C LEU* 4.2 0.7 - - - -
29C PHE* 5.7 1.3 - - - -
45C PRO* 5.7 0.4 - - - -
46C HIS* 4.0 6.1 - - - -
65C GLN* 4.6 11.9 - - - -
70C VAL* 3.8 10.8 - - - +
72C ALA 2.9 13.0 + - - +
73C ILE* 4.2 11.7 - - - -
74C PHE* 2.8 28.6 + - - +
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Residues in contact with GLY 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLY* 1.3 73.3 - - - -
17C LEU* 1.3 65.2 + - - +
18C PHE* 3.6 19.5 + - - -
29C PHE* 5.5 2.9 - - - -
45C PRO* 6.1 0.2 - - - -
46C HIS 3.1 14.1 + - - +
47C ILE* 3.5 10.2 - - - -
48C ASP* 2.8 30.7 + - - +
74C PHE* 3.1 7.0 - - - -
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Residues in contact with LEU 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLY* 4.5 1.6 - - - -
16C GLY* 1.3 79.4 - - - +
18C PHE* 1.3 62.2 + - - +
19C PRO* 3.6 2.5 - - - +
48C ASP* 3.7 11.7 - - + +
58C VAL* 4.6 22.9 - - + +
61C ALA* 4.2 37.5 - - + +
62C PHE* 4.8 3.6 - - + +
65C GLN* 5.1 3.8 - - + -
73C ILE* 3.6 25.6 - - + -
74C PHE 2.8 9.3 + - - -
75C GLY* 3.1 25.1 - - - -
76C PHE* 3.3 18.2 + - - +
85C ILE* 4.6 12.1 - - + -
96C PHE* 4.6 7.2 - - + -
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Residues in contact with PHE 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C GLY* 3.6 19.5 + - - -
17C LEU* 1.3 75.1 - - - +
19C PRO* 1.3 69.0 - - + +
22C ALA* 4.4 9.2 - - + +
25C GLU 4.0 6.5 - - - -
26C TYR* 3.7 49.8 - + + -
29C PHE* 3.4 22.9 - + + -
47C ILE* 4.1 12.8 - - + -
48C ASP 3.4 7.8 + - - -
49C ASN* 3.3 36.9 - - - +
50C LEU 3.6 2.6 + - - -
74C PHE* 3.3 38.6 - + - -
76C PHE* 3.9 13.7 - + - -
285C THR* 4.4 0.9 - - + -
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Residues in contact with PRO 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LEU 3.6 2.5 - - - +
18C PHE* 1.3 85.7 - - + +
20C ARG* 1.3 69.6 + - - +
22C ALA* 3.0 28.8 + - + +
50C LEU 3.4 10.3 - - - +
52C VAL* 3.7 36.3 - - + +
76C PHE* 3.4 37.9 - - + +
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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