Contacts of the helix formed by residues 15 - 27 (chain C) in PDB entry 4UU9
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 HIS 15 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A TYR* 5.0 3.6 - + - -
95A ASP 5.0 1.1 - - - -
96A ASP* 3.5 32.1 - - + +
100A TYR* 2.7 53.0 + - + +
101A ASP* 3.7 31.2 - - + -
46B LEU* 3.7 9.0 - - + -
14C LYS* 1.3 77.7 - - + +
16C SER* 1.3 63.3 + - - +
17C VAL* 3.2 26.4 + - + +
18C VAL* 3.0 11.8 + - + +
19C LYS* 3.0 21.9 + - - +
46C ARG* 3.7 9.6 - - - +
1065C SO4 3.0 16.3 + - - +
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Residues in contact with SER 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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94A ARG* 3.7 7.6 + - - +
101A ASP* 2.9 38.7 + - - +
102A VAL* 5.1 1.4 - - - +
48B ILE* 4.2 16.1 - - - +
14C LYS 3.8 1.4 + - - -
15C HIS* 1.3 72.0 + - - +
17C VAL* 1.3 56.5 + - - +
19C LYS* 3.7 12.8 - - - +
20C LYS* 2.9 31.6 + - - +
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Residues in contact with VAL 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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100A TYR* 4.1 33.2 - - + +
32B TYR* 3.9 21.1 - - - +
46B LEU* 4.2 4.7 - - + -
47B ILE 5.3 0.4 - - - +
48B ILE* 4.1 25.4 - - + -
49B PHE 5.9 0.7 - - - +
15C HIS* 3.2 25.8 + - + +
16C SER* 1.3 76.4 - - - +
18C VAL* 1.3 59.2 + - + +
20C LYS* 3.5 7.3 + - - +
21C CYS* 3.1 28.7 + - - -
43C LEU* 4.4 19.3 - - + -
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Residues in contact with VAL 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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100A TYR* 3.6 30.5 - - + -
13C TYR* 3.6 24.0 - - + -
15C HIS* 3.0 9.0 + - + +
17C VAL* 1.3 75.4 - - + +
19C LYS* 1.3 64.0 + - - +
21C CYS* 3.1 16.9 + - - +
22C CYS 3.1 9.7 + - - -
46C ARG* 3.5 19.3 - - + +
47C CYS* 4.4 1.1 - - - +
50C ALA* 3.5 25.6 - - + +
1065C SO4 3.6 27.1 - - - +
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Residues in contact with LYS 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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32A TYR* 4.6 4.4 + - - -
94A ARG* 5.2 4.9 - - - +
10C ALA* 3.1 23.8 + - + +
11C ALA* 3.7 14.8 + - - +
13C TYR* 2.6 33.7 + - - +
14C LYS 3.7 14.1 - - - -
15C HIS 3.0 13.8 + - - +
16C SER* 3.7 13.2 - - - +
18C VAL* 1.3 77.0 - - - +
20C LYS* 1.3 62.1 + - - +
22C CYS* 3.1 10.5 + - - +
23C TYR* 3.0 44.1 + - + +
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Residues in contact with LYS 20 (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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48B ILE* 3.6 27.6 - - + -
49B PHE 3.8 18.2 - - - +
50B ASP* 2.9 28.8 + - - -
51B VAL* 5.8 0.7 - - + +
16C SER 2.9 16.4 + - - +
17C VAL 3.6 6.5 - - - +
19C LYS* 1.3 76.6 - - - +
21C CYS* 1.3 58.2 + - - +
23C TYR* 3.3 14.1 + - + +
24C ASP* 2.9 52.1 + - - +
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Residues in contact with CYS 21 (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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49B PHE 5.9 0.7 - - - -
51B VAL* 4.2 5.8 - - - -
17C VAL* 3.1 19.5 + - - -
18C VAL 3.1 12.6 + - - +
20C LYS* 1.3 76.9 - - - +
22C CYS* 1.3 60.3 + - - +
24C ASP* 3.5 4.6 + - - -
25C GLY 3.0 17.7 + - - -
43C LEU* 4.0 14.1 - - - -
47C CYS* 2.0 64.4 - - + +
51C PHE* 3.4 17.0 - - + +
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Residues in contact with CYS 22 (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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6C ILE* 3.8 17.9 - - - -
10C ALA* 3.8 24.7 - - + -
13C TYR* 5.1 0.9 - - + -
18C VAL 3.1 9.2 + - - +
19C LYS* 3.1 10.2 + - - +
21C CYS* 1.3 77.2 - - - +
23C TYR* 1.3 63.1 + - - +
25C GLY 3.0 10.7 + - - -
26C ALA* 3.0 10.7 + - - +
50C ALA* 3.7 17.8 - - + +
54C CYS* 2.0 53.9 - - - +
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Residues in contact with TYR 23 (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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6C ILE* 3.8 20.6 - - + -
7C GLU* 4.4 23.0 + - + +
10C ALA* 3.7 25.0 - - + +
19C LYS* 3.0 37.3 + - + +
20C LYS* 3.8 14.6 - - + +
22C CYS* 1.3 75.8 - - - +
24C ASP* 1.3 65.5 + - - +
26C ALA* 3.2 15.5 + - - +
27C CYS* 3.3 10.6 + - - +
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Residues in contact with ASP 24 (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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50B ASP* 3.7 7.6 - - - +
51B VAL* 2.8 41.1 + - + -
52B ASN* 3.0 33.6 + - - +
20C LYS* 2.9 46.1 + - - +
21C CYS 3.8 4.3 - - - +
23C TYR* 1.3 76.8 - - - +
25C GLY* 1.3 62.4 + - - +
27C CYS* 3.1 7.8 + - - -
37C ARG* 3.0 17.7 + - - -
51C PHE* 3.9 2.0 - - - -
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Residues in contact with GLY 25 (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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21C CYS 3.0 11.5 + - - -
22C CYS 3.0 4.7 + - - -
24C ASP* 1.3 77.4 - - - +
26C ALA* 1.3 58.9 + - - +
27C CYS 3.3 1.6 + - - +
37C ARG* 3.5 7.1 + - - -
51C PHE* 3.4 37.4 - - - -
55C CYS* 3.3 29.0 - - - +
58C ALA* 5.1 0.2 - - - +
62C ARG* 5.2 0.5 + - - -
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Residues in contact with ALA 26 (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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2C LEU* 5.7 0.7 - - + -
6C ILE* 3.8 40.8 - - + -
22C CYS 3.0 10.6 + - - +
23C TYR* 3.2 8.9 + - - +
25C GLY* 1.3 74.3 - - - +
27C CYS* 1.3 59.8 + - - +
54C CYS* 3.9 3.9 - - + +
58C ALA* 3.8 11.9 - - + -
62C ARG* 2.9 32.6 + - - -
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Residues in contact with CYS 27 (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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52B ASN* 3.5 17.0 - - - +
23C TYR 3.3 7.8 + - - +
24C ASP* 3.1 19.3 + - - +
25C GLY 3.6 0.5 - - - +
26C ALA* 1.3 77.1 - - - +
28C VAL* 1.3 78.8 + - - +
29C ASN 3.5 0.2 + - - -
37C ARG* 3.1 24.2 + - - +
62C ARG* 4.1 1.7 + - - -
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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