Contacts of the helix formed by residues 14 - 30 (chain B) in PDB entry 1URP
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 PRO 14 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ASN 4.4 2.2 - - - +
13B ASN* 1.3 90.7 - - - +
15B PHE* 1.3 64.2 + - - +
17B VAL* 3.1 8.4 + - + +
18B SER* 2.9 29.0 + - - -
218B PRO* 6.0 6.3 - - + -
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Residues in contact with PHE 15 (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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13B ASN* 2.8 23.6 + - - +
14B PRO* 1.3 72.8 - - - +
16B PHE* 1.3 91.2 + + - +
18B SER 3.4 0.3 + - - -
19B LEU* 3.0 27.7 + - + +
89B ASP* 3.6 26.7 - - - -
215B ASP 5.9 1.3 - - - -
235B GLN* 3.8 39.0 - - + -
237B PRO* 3.0 44.9 - - + +
240B ILE* 4.2 7.9 - - + -
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Residues in contact with PHE 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 4.1 8.2 - - + +
9B SER* 3.7 10.8 - - - -
10B THR* 3.0 37.9 - - + +
11B LEU* 3.9 4.7 - - - +
13B ASN* 3.2 36.5 + - - +
15B PHE* 1.3 100.8 - + - +
17B VAL* 1.3 62.3 + - - +
19B LEU* 3.6 9.1 - - + +
20B LYS* 3.0 26.0 + - - +
64B ASN* 3.3 38.8 - - - -
89B ASP* 3.8 12.8 - - + -
90B ARG* 4.0 18.6 - - - -
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Residues in contact with VAL 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU* 3.5 41.3 - - + +
13B ASN 3.1 13.1 + - - +
14B PRO* 3.1 10.7 + - + +
16B PHE* 1.3 73.2 - - - +
18B SER* 1.3 61.1 + - - +
20B LYS* 3.2 11.2 + - - +
21B ASP* 2.8 49.1 + - - +
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Residues in contact with SER 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B PRO* 2.9 15.0 + - - +
15B PHE 3.6 1.8 - - - -
17B VAL* 1.3 74.2 - - - +
19B LEU* 1.3 59.9 + - - +
21B ASP* 3.2 8.9 + - - +
22B GLY 2.8 27.0 + - - -
237B PRO* 3.6 25.7 - - - +
238B ASP* 3.2 19.4 - - - +
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Residues in contact with LEU 19 (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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6B LEU* 4.3 16.4 - - + -
8B VAL* 4.7 8.5 - - + -
15B PHE* 3.0 26.2 + - + +
16B PHE* 3.6 25.6 - - + +
17B VAL 3.3 0.2 - - - -
18B SER* 1.3 75.4 - - - +
20B LYS* 1.3 64.4 + - - +
22B GLY 3.5 0.2 + - - -
23B ALA* 3.2 17.3 + - - +
64B ASN* 4.8 4.0 - - + -
88B LEU* 3.7 31.6 - - + -
89B ASP* 4.7 6.5 - - + -
237B PRO 3.3 17.9 - - - +
240B ILE* 3.8 25.4 - - + -
241B GLY* 3.5 12.0 - - - +
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Residues in contact with LYS 20 (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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6B LEU* 4.0 15.7 - - + -
8B VAL* 5.4 1.8 - - + -
11B LEU* 3.5 31.2 - - + -
16B PHE 3.0 13.2 + - - +
17B VAL* 3.6 15.2 - - - +
19B LEU* 1.3 78.1 - - - +
21B ASP* 1.3 78.8 + - - +
23B ALA* 3.2 3.1 + - - +
24B GLN* 2.8 32.2 + - + +
34B LEU* 4.6 0.5 - - - +
36B VAL* 3.8 39.0 - - + -
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Residues in contact with ASP 21 (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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17B VAL* 2.8 34.9 + - - +
18B SER* 3.6 8.2 - - - +
20B LYS* 1.3 94.2 + - - +
22B GLY* 1.3 57.0 + - - +
24B GLN* 3.2 7.8 + - - +
25B LYS* 2.9 32.0 + - - +
238B ASP* 5.6 0.9 - - + -
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Residues in contact with GLY 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B SER 2.8 16.5 + - - -
19B LEU 3.9 0.2 - - - -
21B ASP* 1.3 70.9 - - - +
23B ALA* 1.3 56.3 + - - +
25B LYS* 3.6 5.1 + - - +
26B GLU* 3.1 23.4 + - - +
238B ASP* 3.3 31.9 - - - +
242B ALA* 3.5 19.5 - - - +
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Residues in contact with ALA 23 (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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6B LEU* 4.1 20.4 - - + -
19B LEU* 3.2 14.8 + - + +
20B LYS 3.2 8.0 + - - +
22B GLY* 1.3 72.2 - - - +
24B GLN* 1.3 61.7 + - - +
27B ALA* 3.0 31.2 + - - +
34B LEU* 4.0 6.3 - - + -
62B LEU* 5.2 2.5 - - + -
241B GLY* 3.5 25.2 - - - +
242B ALA* 4.3 0.4 - - - +
245B VAL* 3.4 15.7 - - + +
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Residues in contact with GLN 24 (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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20B LYS* 2.8 20.3 + - + +
21B ASP* 3.5 8.5 - - - +
23B ALA* 1.3 74.1 - - - +
25B LYS* 1.3 66.4 + - - +
27B ALA* 3.2 4.2 + - - +
28B ASP* 2.9 58.2 + - - +
32B TYR 5.3 0.4 + - - -
34B LEU* 3.8 41.1 + - + +
36B VAL* 4.6 5.9 - - - +
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Residues in contact with LYS 25 (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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21B ASP 2.9 16.1 + - - +
22B GLY* 4.0 6.1 - - - +
24B GLN* 1.3 77.1 - - - +
26B GLU* 1.3 60.7 + - - +
28B ASP* 3.4 9.2 + - - +
29B LYS* 3.1 55.5 + - - +
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Residues in contact with GLU 26 (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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22B GLY 3.1 18.3 + - - +
23B ALA 4.1 2.5 - - - +
25B LYS* 1.3 75.2 - - - +
27B ALA* 1.3 57.6 + - - +
29B LYS* 3.3 27.0 + - - +
30B LEU* 3.0 49.7 + - + +
242B ALA* 3.4 38.3 - - + +
245B VAL* 3.9 11.4 - - + -
246B GLU* 3.5 17.2 - - - +
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Residues in contact with ALA 27 (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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4B ILE* 5.5 0.4 - - + -
23B ALA 3.0 19.1 + - - +
24B GLN* 3.2 5.6 + - - +
26B GLU* 1.3 73.9 - - - +
28B ASP* 1.3 63.7 + - - +
30B LEU* 3.3 1.9 + - - -
31B GLY 3.0 5.4 + - - -
32B TYR* 2.8 42.8 + - + +
34B LEU* 4.1 24.7 - - + -
245B VAL* 3.6 19.4 - - + +
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Residues in contact with ASP 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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1B LYS* 5.5 3.5 + - - +
24B GLN* 2.9 47.1 + - - +
25B LYS* 3.6 9.4 - - + +
27B ALA* 1.3 75.0 - - - +
29B LYS* 1.3 64.0 + - - +
31B GLY* 3.2 13.2 + - - -
32B TYR 4.4 8.3 - - - +
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Residues in contact with LYS 29 (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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25B LYS* 3.1 45.8 + - - +
26B GLU* 3.4 29.5 + - - +
28B ASP* 1.3 81.9 - - - +
30B LEU* 1.3 65.9 + - + +
31B GLY 3.6 0.2 + - - -
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Residues in contact with LEU 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 GLU* 3.0 44.8 + - + +
27B ALA* 3.3 0.6 + - - -
29B LYS* 1.3 83.8 - - + +
31B GLY* 1.3 60.4 + - - +
32B TYR* 3.6 22.4 - - + -
245B VAL* 4.4 3.8 - - + -
246B GLU* 3.9 16.4 - - + +
249B ASP* 3.7 38.2 - - + +
253B LYS* 5.0 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
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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