Contacts of the strand formed by residues 41 - 48 (chain C) in PDB entry 2UUG
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 41 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ILE 3.9 0.2 - - - +
23C LEU* 3.4 4.2 - - - +
24C MET* 2.7 43.3 + - - +
29C VAL* 4.2 10.3 - - + -
37C PRO* 3.6 39.7 - - + -
39C SER 3.7 3.4 - - - +
40C ASP* 1.3 78.6 - - - +
42C LEU* 1.3 68.3 + - - +
43C VAL* 4.5 4.7 - - + +
58C LEU* 3.7 33.7 - - + -
59C THR 3.3 20.0 - - - +
60C SER* 4.2 5.4 - - - -
68C TRP* 4.3 20.6 - - + -
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ASP* 6.1 0.2 - - - +
133A ALA* 4.2 8.1 - - + +
134A HIS* 4.1 14.8 - - + -
21C SER* 4.0 18.2 - - - +
22C ILE 3.6 0.7 - - - -
23C LEU* 3.9 29.8 - - + +
41C ILE* 1.3 73.9 - - - +
43C VAL* 1.3 61.1 + - - +
44C HIS* 3.3 23.7 + - + +
58C LEU* 3.4 1.4 - - - -
59C THR* 2.8 32.7 + - - +
60C SER 3.9 9.2 + - - +
61C ASP* 3.5 25.8 - - - +
62C ALA 4.0 0.2 - - - +
65C TYR* 3.6 31.4 - - + -
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Residues in contact with VAL 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A SER* 4.2 13.7 - - - +
191A LEU* 3.7 29.4 - - + -
21C SER* 3.4 1.1 - - - -
22C ILE* 2.8 41.2 + - + +
24C MET* 4.2 19.5 - - + -
29C VAL* 4.7 0.2 - - + -
41C ILE* 4.6 4.3 - - + -
42C LEU* 1.3 72.3 - - - +
44C HIS* 1.3 57.1 + - - +
45C THR* 3.2 23.8 + - - +
56C MET* 3.8 24.5 - - + -
57C LEU 4.0 1.8 - - - -
58C LEU* 3.9 16.6 - - + -
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Residues in contact with HIS 44 (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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67A HIS* 5.5 1.0 - + - -
133A ALA* 4.4 3.4 - - + -
4C LEU* 3.4 27.3 - - + +
8C ILE* 5.3 1.2 - - - +
18C ILE* 3.8 23.2 - - + +
20C GLU 3.7 5.2 - - - -
21C SER* 2.8 30.1 + - - +
42C LEU* 3.3 22.1 - - + +
43C VAL* 1.3 68.2 - - - +
45C THR* 1.3 60.6 + - - +
46C ALA 4.1 0.2 + - - -
55C VAL 3.6 1.7 - - - +
56C MET* 3.1 3.0 - - - -
57C LEU* 2.7 60.9 + - + +
59C THR* 2.6 39.4 + - + -
65C TYR* 4.1 13.6 - + - -
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Residues in contact with THR 45 (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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87A PRO* 3.7 26.9 - - + +
189A SER* 4.2 6.1 + - - -
190A PRO* 4.0 10.1 - - + -
18C ILE* 3.8 2.2 - - - +
19C GLN* 3.0 26.2 + - - +
20C GLU* 2.9 35.4 + - - +
22C ILE* 5.3 0.5 - - - +
43C VAL* 3.4 15.4 + - - +
44C HIS* 1.3 72.2 - - - +
46C ALA* 1.3 63.0 + - - +
54C ASN* 4.1 6.7 - - - +
55C VAL 3.7 2.5 - - - +
56C MET* 3.6 26.1 - - + +
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Residues in contact with ALA 46 (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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87A PRO* 4.9 0.7 - - - -
8C ILE* 4.4 13.0 - - + -
16C LEU* 4.0 24.2 - - + -
17C VAL 3.4 25.6 - - - +
18C ILE* 4.2 2.9 - - - -
19C GLN* 4.5 1.6 - - - +
45C THR* 1.3 77.3 - - - +
47C TYR* 1.3 61.8 + - - +
54C ASN* 3.7 3.5 - - - +
55C VAL* 2.9 37.3 + - - +
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Residues in contact with TYR 47 (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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85A ILE 6.0 2.9 - - - +
87A PRO* 4.5 8.2 - - + +
90A LEU* 5.4 19.3 - - + -
16C LEU* 4.0 11.9 - - - +
17C VAL 4.7 1.6 + - - +
19C GLN* 3.6 24.6 + - - +
46C ALA* 1.3 74.6 - - - +
48C ASP* 1.3 60.2 + - - +
49C GLU* 3.7 34.2 + - + +
52C ASP* 2.7 42.1 + - - +
53C GLU 3.2 19.7 - - - -
54C ASN* 3.7 19.7 - - - +
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Residues in contact with ASP 48 (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 LYS* 3.6 25.2 - - + +
16C LEU* 3.4 32.4 - - + +
46C ALA 4.2 0.4 + - - -
47C TYR* 1.3 74.0 - - - +
49C GLU* 1.3 63.0 + - - +
50C SER* 2.8 31.5 + - - -
51C THR* 2.9 32.8 + - - +
52C ASP 2.9 9.5 + - - -
53C GLU* 3.1 18.3 + - + +
55C VAL* 4.9 2.7 - - + -
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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