Contacts of the strand formed by residues 35 - 40 (chain C) in PDB entry 3UDB
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 ALA 35 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU* 4.3 11.9 - - - +
26C ASP* 3.7 2.8 - - - -
27C ILE* 2.7 44.7 + - + +
34C VAL* 1.3 80.5 - - - +
36C ARG* 1.3 64.0 + - - +
37C LEU* 5.5 0.9 - - + -
48C ALA* 5.1 7.4 - - + -
49C VAL 3.5 18.4 - - - +
50C LYS* 4.3 9.4 - - + +
51C TYR* 5.8 1.6 - - - -
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Residues in contact with ARG 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.7 15.4 - - + +
13C PRO* 3.2 34.1 + - - +
14C ILE* 4.3 1.8 - - - +
15C MET* 4.3 14.8 - - - +
23C LEU* 3.4 37.7 - - + +
25C LYS 3.9 2.7 - - - +
26C ASP* 2.6 52.3 + - - +
35C ALA* 1.3 77.1 - - - +
37C LEU* 1.3 63.6 + - - +
38C MET* 3.2 28.1 - - - +
48C ALA* 3.5 1.4 - - - -
49C VAL* 2.9 34.3 + - + +
51C TYR* 3.2 32.4 + - + -
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Residues in contact with LEU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 3.6 3.5 - - - +
24C VAL* 2.9 33.7 + - + -
25C LYS 3.0 16.9 + - - +
27C ILE* 3.6 31.4 - - + -
35C ALA* 5.5 1.3 - - + -
36C ARG* 1.3 76.7 - - - +
38C MET* 1.3 64.7 + - - +
46C LEU* 4.9 4.3 - - + -
47C VAL 3.5 7.6 - - - +
48C ALA* 4.2 6.5 - - + -
96C TYR* 3.9 54.5 - - + +
107D CYS 5.1 1.3 - - - +
109D ALA 4.5 2.0 - - - -
110D GLY* 3.9 25.6 - - - +
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Residues in contact with MET 38 (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 MET* 3.7 17.0 - - + -
16C HIS* 3.7 12.8 - - + +
21C TYR* 3.6 35.4 - - + -
22C GLU 3.2 13.0 - - - +
23C LEU* 4.3 4.3 - - - -
24C VAL* 3.8 6.7 - - - -
36C ARG* 3.2 32.1 - - - +
37C LEU* 1.3 81.1 - - - +
39C ARG* 1.3 62.0 + - - +
40C ASP 4.0 0.2 - - - -
46C LEU* 3.5 3.1 - - - +
47C VAL* 2.8 42.9 + - + +
49C VAL* 3.8 20.4 - - + -
51C TYR* 3.4 17.5 - - - +
93C VAL* 6.1 0.2 - - - -
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Residues in contact with ARG 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TYR* 3.3 3.3 - - - -
22C GLU* 2.7 66.6 + - - +
24C VAL* 3.7 15.2 - - + +
38C MET* 1.3 73.4 - - - +
40C ASP* 1.3 65.7 + - - +
41C LYS* 3.3 39.1 + - - +
44C ASN* 3.2 44.4 + - - +
45C GLU* 3.6 15.7 - - - +
46C LEU* 4.5 5.4 - - + +
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Residues in contact with ASP 40 (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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20C ARG* 4.4 9.4 + - - +
21C TYR* 3.0 38.6 + - + -
38C MET 4.0 1.0 + - - -
39C ARG* 1.3 70.7 - - - +
41C LYS* 1.3 64.1 + - - +
42C GLN* 2.3 33.6 + - - +
43C ALA* 3.6 10.1 - - - +
44C ASN* 3.2 15.6 + - - -
45C GLU* 3.1 22.9 + - - +
47C VAL* 5.0 6.5 - - + +
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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