Contacts of the helix formed by residues 15 - 31 (chain C) in PDB entry 5U03
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 GLY 15 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C GLY 3.2 1.2 - - - -
14C ILE* 1.4 81.3 - - - +
16C LYS* 1.3 68.6 + - - +
17C GLY 3.3 2.0 - - - -
18C ILE* 3.2 6.2 + - - +
19C ILE* 3.0 30.4 + - - +
180C VAL* 5.0 2.0 - - - -
601C ATP 2.9 35.7 + - - -
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Residues in contact with LYS 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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6C VAL* 3.9 18.3 - - + +
7C THR 3.7 30.1 - - - +
8C GLY* 3.7 9.4 + - - +
11C ILE 6.1 0.2 - - - -
12C SER* 6.2 2.7 - - - +
14C ILE* 3.7 18.2 - - + -
15C GLY* 1.3 76.6 - - - +
17C GLY* 1.3 58.3 + - - +
19C ILE* 3.2 3.5 + - - +
20C ALA* 2.8 29.4 + - - +
146C GLU* 4.4 9.4 - - + +
147C LEU 2.8 25.4 + - - +
148C GLY* 3.6 7.6 - - - -
149C GLY 2.5 31.9 + - - +
150C THR* 5.9 1.8 - - - -
180C VAL* 4.0 12.6 - - + -
601C ATP 3.1 19.5 + - - +
602C UTP 5.0 5.8 - - - -
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Residues in contact with GLY 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LYS* 1.3 76.3 - - - +
18C ILE* 1.3 57.2 + - - +
21C SER* 2.9 30.7 + - - -
70C ASP* 4.4 6.3 - - - -
73C ASN* 5.7 2.9 - - - +
74C TYR* 3.5 25.2 - - - -
146C GLU* 3.6 10.5 + - - -
601C ATP 3.0 19.9 + - - -
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Residues in contact with ILE 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C GLY* 3.2 9.2 + - - +
16C LYS 3.1 0.8 - - - -
17C GLY* 1.3 77.9 - - - +
19C ILE* 1.3 61.9 + - + +
21C SER* 2.8 21.3 + - - +
22C SER* 2.9 16.1 + - - +
73C ASN* 5.2 12.1 - - + +
77C PHE* 6.5 0.4 - - + -
250C ILE* 3.7 49.1 - - + -
253C VAL* 4.4 14.4 - - + -
601C ATP 3.5 57.4 + - + +
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Residues in contact with ILE 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C VAL* 5.7 3.1 - - + -
15C GLY 3.0 17.4 + - - +
16C LYS* 3.8 4.3 - - - +
18C ILE* 1.3 75.4 - - + +
20C ALA* 1.3 62.6 + - - +
22C SER* 3.0 3.7 + - - -
23C VAL* 2.8 44.5 + - + +
178C ILE* 5.2 7.9 - - + -
180C VAL* 4.8 7.4 - - + -
215C VAL* 4.2 41.7 - - + -
244C VAL* 4.3 15.3 - - + -
253C VAL* 3.9 24.5 - - + -
257C LEU* 4.9 9.2 - - + -
601C ATP 5.7 2.9 - - - +
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Residues in contact with ALA 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C VAL* 4.5 10.1 - - + +
16C LYS 2.8 16.5 + - - +
17C GLY* 3.7 0.9 - - - +
19C ILE* 1.3 78.9 - - - +
21C SER* 1.3 52.0 + - - +
23C VAL* 3.3 4.0 + - - +
24C GLY* 2.7 32.6 + - - -
74C TYR* 3.3 29.6 - - + +
144C VAL* 4.0 28.1 - - + +
146C GLU* 5.1 3.4 - - + -
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Residues in contact with SER 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLY 2.9 13.7 + - - -
18C ILE* 2.8 24.9 + - - +
20C ALA* 1.3 75.3 - - - +
22C SER* 1.3 64.4 + - - +
24C GLY* 3.8 1.5 - - - -
25C THR 3.1 17.7 + - - -
73C ASN* 4.6 5.5 - - - +
74C TYR* 3.6 22.6 - - - -
77C PHE* 3.2 49.0 - - - +
78C LEU* 4.3 1.7 - - - +
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Residues in contact with SER 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ILE* 2.9 14.9 + - - +
19C ILE 3.0 7.2 + - - -
21C SER* 1.3 80.7 + - - +
23C VAL* 1.3 62.3 + - - +
25C THR* 3.3 4.7 - - - +
26C ILE* 3.1 28.2 + - - +
77C PHE* 4.1 11.2 - - - -
250C ILE* 4.8 1.6 + - - +
253C VAL* 3.4 24.6 - - - +
254C PRO* 3.8 15.0 - - - +
257C LEU* 3.7 18.8 - - - -
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Residues in contact with VAL 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 4.9 6.7 - - + -
19C ILE* 2.8 35.1 + - + +
20C ALA* 3.9 4.7 - - - +
22C SER* 1.3 73.6 - - - +
24C GLY* 1.3 67.4 + - - +
26C ILE* 3.0 12.5 + - + +
27C LEU* 2.7 45.6 + - + +
144C VAL* 5.1 5.4 - - + -
178C ILE* 6.6 0.2 - - + -
257C LEU* 3.9 15.9 - - + -
262C VAL* 5.6 1.6 - - + -
266C PHE* 4.2 30.7 - - + -
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Residues in contact with GLY 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ALA 2.7 17.5 + - - -
21C SER 3.8 1.8 - - - -
22C SER 3.2 0.2 - - - -
23C VAL* 1.3 76.9 - - - +
25C THR* 1.4 55.5 + - - +
27C LEU* 3.0 9.5 + - - +
28C LYS 2.9 22.9 + - - -
34C VAL* 3.7 17.3 - - - +
78C LEU* 3.6 19.6 - - - +
144C VAL* 4.9 4.3 - - - -
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Residues in contact with THR 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C SER 3.1 14.1 + - - +
22C SER* 3.3 12.3 - - - +
24C GLY* 1.4 72.1 - - - +
26C ILE* 1.3 69.0 + - + +
28C LYS* 3.3 5.5 + - - +
29C SER* 2.8 27.7 + - - -
77C PHE* 2.7 32.9 + - + +
78C LEU* 3.8 9.4 - - - +
254C PRO* 4.9 2.0 - - + -
284C LYS* 3.9 14.9 + - - -
285C TRP* 3.8 33.0 + - + +
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Residues in contact with ILE 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C SER 3.1 20.0 - - - +
23C VAL* 3.0 11.8 + - + +
25C THR* 1.3 87.9 - - + +
27C LEU* 1.3 61.4 + - + +
29C SER* 3.0 9.1 + - - -
30C CYS* 2.8 33.0 + - - -
254C PRO* 4.1 8.7 - - + +
257C LEU* 3.7 34.5 - - + -
262C VAL* 5.2 2.0 - - + -
263C VAL* 3.6 30.5 - - + -
266C PHE* 6.4 0.7 - - + -
280C LYS* 3.6 33.4 - - + +
285C TRP* 6.0 0.4 - - - +
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Residues in contact with LEU 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 3.8 29.6 - - + -
23C VAL* 2.7 35.0 + - + +
24C GLY* 3.5 3.8 - - - +
26C ILE* 1.3 75.4 - - + +
28C LYS* 1.3 60.3 + - - +
30C CYS* 3.2 15.1 + - - +
31C GLY 3.0 5.9 + - - -
32C LEU* 3.0 41.8 + - + +
34C VAL* 3.5 15.7 - - + -
142C VAL* 3.9 18.6 - - + -
144C VAL* 4.1 10.3 - - + -
263C VAL* 6.2 1.6 - - + -
266C PHE* 5.1 15.9 - - + -
270C LEU* 5.8 1.1 - - + -
272C LEU* 5.5 3.8 - - + -
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Residues in contact with LYS 28 (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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24C GLY 2.9 11.9 + - - +
25C THR* 3.6 11.0 - - - +
26C ILE 3.2 0.2 - - - -
27C LEU* 1.3 74.3 - - - +
29C SER* 1.3 64.9 + - - +
31C GLY* 2.9 15.7 + - - -
32C LEU 3.3 22.0 + - - +
33C HIS* 4.7 8.7 - - - +
34C VAL* 3.5 6.2 - - + +
77C PHE 5.9 0.2 - - - +
78C LEU* 3.9 22.7 - - + -
79C ASP* 5.9 8.7 - - - +
80C ILE* 5.4 6.6 - - + +
134C ASP* 2.8 28.0 + - - -
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Residues in contact with SER 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C THR 2.8 14.4 + - - -
26C ILE* 3.2 11.2 - - - -
28C LYS* 1.3 77.9 - - - +
30C CYS* 1.3 62.2 + - - +
31C GLY* 3.2 1.9 + - - -
279C ARG 5.5 1.0 - - - +
280C LYS* 3.4 14.2 - - - +
281C MET* 3.1 40.2 + - - +
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Residues in contact with CYS 30 (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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26C ILE* 2.8 30.5 + - - -
27C LEU* 3.2 18.8 - - - +
28C LYS 3.2 0.2 - - - -
29C SER* 1.3 75.5 - - - +
31C GLY* 1.3 58.7 + - - +
32C LEU* 4.6 10.5 - - + -
263C VAL* 4.0 21.5 - - - -
267C LEU* 5.6 3.8 - - + -
274C ILE* 3.9 38.7 - - + +
275C GLU 4.6 7.0 + - - +
279C ARG 5.5 2.5 - - - -
280C LYS* 5.3 5.6 - - - -
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Residues in contact with GLY 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU 3.0 0.2 + - - -
28C LYS* 2.9 14.3 + - - -
29C SER 4.0 1.6 - - - -
30C CYS* 1.3 80.4 - - - +
32C LEU* 1.3 68.6 + - - +
141C GLN* 3.6 7.4 + - - +
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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
------------------------------------------------------------
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