Contacts of the helix formed by residues 15 - 31 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLY 3.2 1.2 - - - -
14B ILE* 1.4 82.7 - - - +
16B LYS* 1.3 67.1 + - - +
17B GLY 3.3 2.0 - - - -
18B ILE* 3.2 6.8 + - - +
19B ILE* 3.0 30.5 + - - +
180B VAL* 5.0 2.0 - - - -
601B ATP 2.9 35.6 + - - -
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Residues in contact with LYS 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 3.9 17.5 - - + +
7B THR 3.7 30.5 - - - +
8B GLY* 3.7 9.6 + - - +
11B ILE 6.1 0.2 - - - -
12B SER* 6.2 2.9 - - - +
14B ILE* 3.7 17.7 - - + -
15B GLY* 1.3 77.8 - - - +
17B GLY* 1.3 57.6 + - - +
19B ILE* 3.2 3.5 + - - +
20B ALA* 2.8 29.9 + - - +
146B GLU* 4.4 10.1 - - + +
147B LEU 2.8 25.5 + - - +
148B GLY* 3.6 7.6 - - - -
149B GLY 2.5 31.3 + - - +
150B THR* 5.9 1.3 - - - -
180B VAL* 4.0 11.9 - - + -
601B ATP 3.1 18.7 + - - +
602B UTP 5.0 5.6 - - - -
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Residues in contact with GLY 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LYS* 1.3 74.9 - - - +
18B ILE* 1.3 58.7 + - - +
21B SER* 2.9 30.7 + - - -
70B ASP* 4.4 6.3 - - - -
73B ASN* 5.7 2.7 - - - +
74B TYR* 3.5 25.5 - - - -
146B GLU* 3.6 9.8 + - - -
601B ATP 3.0 20.1 + - - -
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Residues in contact with ILE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLY* 3.2 8.3 + - - +
16B LYS 3.1 0.6 - - - -
17B GLY* 1.3 77.9 - - - +
19B ILE* 1.3 62.3 + - + +
21B SER* 2.8 21.1 + - - +
22B SER* 2.9 16.1 + - - +
73B ASN* 5.2 12.1 - - + +
77B PHE* 6.5 0.4 - - + -
250B ILE* 3.7 48.2 - - + -
253B VAL* 4.4 14.4 - - + -
601B ATP 3.5 57.2 + - + +
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Residues in contact with ILE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 5.7 3.6 - - + -
15B GLY 3.0 16.5 + - - +
16B LYS* 3.8 4.7 - - - +
18B ILE* 1.3 76.7 - - + +
20B ALA* 1.3 61.5 + - - +
22B SER* 3.0 3.6 + - - -
23B VAL* 2.8 45.0 + - + +
178B ILE* 5.2 7.9 - - + -
180B VAL* 4.8 8.5 - - + -
215B VAL* 4.2 40.6 - - + -
244B VAL* 4.3 14.6 - - + -
253B VAL* 3.9 25.4 - - + -
257B LEU* 4.9 8.7 - - + -
601B ATP 5.7 3.1 - - - +
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Residues in contact with ALA 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 4.5 9.8 - - + +
16B LYS 2.8 16.3 + - - +
17B GLY* 3.7 0.7 - - - +
19B ILE* 1.3 78.6 - - - +
21B SER* 1.3 51.8 + - - +
23B VAL* 3.3 4.3 + - - +
24B GLY* 2.7 32.7 + - - -
74B TYR* 3.3 30.1 - - + +
144B VAL* 4.0 27.2 - - + +
146B GLU* 5.1 3.4 - - + -
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Residues in contact with SER 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLY 2.9 14.4 + - - -
18B ILE* 2.8 24.4 + - - +
20B ALA* 1.3 73.0 - - - +
22B SER* 1.3 64.4 + - - +
24B GLY* 3.8 1.5 - - - +
25B THR 3.1 17.8 + - - -
73B ASN* 4.6 5.9 - - - +
74B TYR* 3.6 23.5 - - - -
77B PHE* 3.2 48.7 - - - +
78B LEU* 4.3 2.1 - - - +
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Residues in contact with SER 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 2.9 14.9 + - - +
19B ILE 3.0 7.6 + - - -
21B SER* 1.3 81.8 + - - +
23B VAL* 1.3 61.1 + - - +
25B THR* 3.3 4.7 - - - +
26B ILE* 3.1 28.0 + - - +
77B PHE* 4.1 11.3 - - - -
250B ILE* 4.8 1.4 + - - +
253B VAL* 3.4 24.8 - - - +
254B PRO* 3.8 14.2 - - - +
257B LEU* 3.7 19.5 - - - -
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 4.9 7.4 - - + -
19B ILE* 2.8 36.0 + - + +
20B ALA* 3.9 4.5 - - - +
22B SER* 1.3 73.6 - - - +
24B GLY* 1.3 67.0 + - - +
26B ILE* 3.0 12.5 + - + +
27B LEU* 2.7 44.2 + - + +
144B VAL* 5.1 5.8 - - + -
178B ILE* 6.6 0.2 - - + -
257B LEU* 3.9 15.3 - - + -
262B VAL* 5.6 2.0 - - + -
266B PHE* 4.2 30.3 - - + -
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Residues in contact with GLY 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ALA 2.7 18.1 + - - -
21B SER 3.3 1.8 + - - -
22B SER 3.2 0.4 - - - -
23B VAL* 1.3 77.5 - - - +
25B THR* 1.4 56.5 + - - +
27B LEU* 3.0 9.6 + - - +
28B LYS 2.9 22.9 + - - -
34B VAL* 3.7 16.9 - - - +
78B LEU* 3.6 20.0 - - - +
144B VAL* 4.9 4.0 - - - -
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Residues in contact with THR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B SER 3.1 14.5 + - - +
22B SER* 3.3 12.3 - - - +
24B GLY* 1.4 71.1 - - - +
26B ILE* 1.3 68.5 + - + +
28B LYS* 3.3 5.3 + - - +
29B SER* 2.8 28.1 + - - -
77B PHE* 2.7 32.8 + - + +
78B LEU* 3.8 9.5 - - - +
254B PRO* 4.9 2.0 - - + -
284B LYS* 3.9 14.6 + - - -
285B TRP* 3.8 32.4 + - + +
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Residues in contact with ILE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B SER 3.1 19.7 - - - +
23B VAL* 3.0 12.5 + - + +
25B THR* 1.3 88.1 - - + +
27B LEU* 1.3 61.2 + - + +
29B SER* 3.0 9.3 + - - -
30B CYS* 2.8 33.5 + - - -
254B PRO* 4.1 9.0 - - + +
257B LEU* 3.7 34.8 - - + -
262B VAL* 5.2 1.6 - - + -
263B VAL* 3.6 29.8 - - + -
266B PHE* 6.4 0.9 - - + -
280B LYS* 3.6 35.7 - - + +
285B TRP* 6.0 0.4 - - - +
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 3.8 30.3 - - + -
23B VAL* 2.7 35.1 + - + +
24B GLY* 3.5 3.1 - - - +
26B ILE* 1.3 75.5 - - + +
28B LYS* 1.3 59.0 + - - +
30B CYS* 3.2 15.1 + - - +
31B GLY 3.0 5.5 + - - -
32B LEU* 3.0 42.0 + - + +
34B VAL* 3.5 15.5 - - + -
142B VAL* 3.9 17.5 - - + -
144B VAL* 4.1 10.5 - - + -
263B VAL* 6.2 1.6 - - + -
266B PHE* 5.1 16.4 - - + -
270B LEU* 5.8 1.3 - - + -
272B LEU* 5.5 4.0 - - + -
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Residues in contact with LYS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLY 2.9 12.5 + - - +
25B THR* 3.6 11.7 - - - +
27B LEU* 1.3 74.0 - - - +
29B SER* 1.3 64.5 + - - +
31B GLY* 2.9 15.5 + - - -
32B LEU 3.3 21.7 + - - +
33B HIS* 4.7 7.9 - - - +
34B VAL* 3.5 6.3 - - + +
77B PHE 5.9 0.2 - - - +
78B LEU* 3.9 22.4 - - + -
79B ASP* 5.9 8.5 - - - +
80B ILE* 5.4 6.7 - - + +
134B ASP* 2.8 29.1 + - - -
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Residues in contact with SER 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B THR 2.8 14.5 + - - -
26B ILE* 3.2 10.8 - - - -
28B LYS* 1.3 77.7 - - - +
30B CYS* 1.3 62.3 + - - +
31B GLY* 3.2 1.6 + - - -
279B ARG 5.5 1.2 - - - +
280B LYS* 3.4 14.2 - - - +
281B MET* 3.1 40.4 + - - +
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Residues in contact with CYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ILE* 2.8 29.8 + - - -
27B LEU* 3.2 17.9 - - - +
28B LYS 3.2 0.2 - - - -
29B SER* 1.3 75.7 - - - +
31B GLY* 1.3 58.3 + - - +
32B LEU* 4.6 10.1 - - + -
263B VAL* 4.0 21.1 - - - -
267B LEU* 5.6 3.4 - - + -
274B ILE* 3.9 37.9 - - + +
275B GLU 4.6 7.2 + - - +
279B ARG* 5.5 2.2 - - - -
280B LYS* 5.2 6.3 - - - +
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Residues in contact with GLY 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LEU 3.0 0.4 + - - -
28B LYS* 2.9 13.8 + - - -
29B SER 4.0 1.8 - - - -
30B CYS* 1.3 80.0 - - - +
32B LEU* 1.3 68.5 + - - +
141B GLN* 3.6 7.8 + - - +
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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
------------------------------------------------------------
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