Contacts of the helix formed by residues 1 - 13 (chain B) in PDB entry 4UY1
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 1 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B ILE* 1.3 62.0 + - - -
3B LEU 3.1 3.7 + - - -
4B GLU* 2.9 18.8 + - - -
5B LEU* 2.8 29.8 + - - +
50B TYR* 4.7 1.3 - - - -
60B PRO 3.3 25.9 + - - -
61B LYS 3.5 12.6 - - - -
62B THR 3.9 4.3 - - - -
63B GLU 2.7 28.0 + - - -
64B ARG* 5.9 0.2 - - - -
65B TYR* 4.0 14.1 - - - -
87B LEU* 4.5 2.2 - - - +
91B ASP* 4.1 2.8 + - - +
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Residues in contact with ILE 2 (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 GLY* 1.3 71.0 - - - -
3B LEU* 1.3 69.1 + - + +
5B LEU* 3.5 10.0 - - + +
6B ALA* 2.9 32.1 + - + +
21B MET* 4.9 7.0 - - + -
50B TYR* 5.5 0.2 - - - -
61B LYS* 3.1 23.9 + - + +
1125B 1PE 4.4 36.6 - - - +
1129B TJM 3.6 28.9 - - + -
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Residues in contact with LEU 3 (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 GLY* 3.1 0.6 - - - -
2B ILE* 1.3 90.7 - - + +
4B GLU* 1.3 65.7 + - - +
6B ALA* 3.5 6.1 + - + +
7B GLY 2.9 17.7 + - - -
64B ARG* 4.0 30.7 - - - +
1131B PEG 2.5 31.3 + - - +
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Residues in contact with GLU 4 (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 GLY* 2.9 27.4 + - - +
3B LEU* 1.3 76.7 - - - +
5B LEU* 1.3 57.9 + - - +
8B THR* 2.7 40.1 + - - +
63B GLU 3.9 1.0 - - - +
64B ARG* 2.8 33.4 + - - -
65B TYR* 3.2 61.3 + - + +
67B TRP* 4.2 2.5 - - - +
1131B PEG 3.1 33.4 - - - -
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Residues in contact with LEU 5 (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 GLY 2.8 17.0 + - - +
2B ILE* 3.5 15.9 - - + +
4B GLU* 1.3 77.8 - - - +
6B ALA* 1.3 61.3 + - - +
8B THR* 3.0 17.4 + - - -
9B VAL* 3.3 15.7 + - + +
46B HIS* 3.7 20.6 - - + +
50B TYR* 3.8 12.6 - - + +
91B ASP* 3.5 29.0 + - + +
94B ILE* 3.9 16.6 - - + -
1125B 1PE 4.7 8.3 - - - +
1129B TJM 3.7 43.3 - - + -
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Residues in contact with ALA 6 (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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2B ILE* 2.9 22.8 + - + +
3B LEU* 3.8 5.8 - - + +
5B LEU* 1.3 74.3 - - - +
7B GLY* 1.3 56.7 + - - +
9B VAL 3.9 0.2 - - - -
10B GLY* 2.9 24.1 + - - -
17B PRO* 3.2 23.9 - - + +
1129B TJM 3.6 24.5 - - + -
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Residues in contact with GLY 7 (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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3B LEU 2.9 17.1 + - - -
4B GLU 3.6 2.7 - - - -
6B ALA* 1.3 77.2 - - - +
8B THR* 1.3 51.5 + - - +
10B GLY* 3.2 1.9 + - - -
11B CYS 2.7 31.0 + - - -
67B TRP* 3.4 18.2 - - - -
1128B DMS 3.5 13.9 - - - +
1131B PEG 3.8 10.8 - - - -
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Residues in contact with THR 8 (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 GLU 2.7 26.7 + - - +
5B LEU 3.0 13.2 + - - -
7B GLY* 1.3 72.4 - - - +
9B VAL* 1.3 61.0 + - - +
11B CYS* 3.4 2.1 + - - +
12B VAL* 3.3 29.6 + - - +
65B TYR* 3.7 17.3 - - + +
67B TRP* 3.7 30.9 - - + -
74B VAL* 3.8 24.4 - - + +
88B CYS* 5.4 0.4 - - - -
91B ASP* 3.6 25.5 + - + +
92B GLN 4.9 1.1 - - - +
95B ALA* 3.5 1.7 - - - +
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Residues in contact with VAL 9 (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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5B LEU* 3.3 17.8 + - + +
6B ALA 4.0 2.5 - - - +
8B THR* 1.3 75.6 + - - +
10B GLY* 1.3 61.1 + - - +
12B VAL* 3.5 0.5 + - - +
13B GLY* 2.9 31.2 + - - +
15B ARG 4.4 5.4 - - - +
17B PRO* 4.1 13.9 - - + -
20B TYR* 3.9 29.8 - - + +
94B ILE* 4.2 10.8 - - + -
95B ALA* 4.1 22.7 - - - +
98B LEU* 4.5 6.5 - - + -
1129B TJM 4.0 23.6 - - + -
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Residues in contact with GLY 10 (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 ALA 2.9 16.4 + - - -
7B GLY* 3.2 4.9 + - - -
9B VAL* 1.3 78.5 - - - +
11B CYS* 1.3 59.9 + - - +
13B GLY* 3.9 6.2 + - - -
15B ARG 5.1 2.7 - - - -
17B PRO* 4.2 14.1 - - - +
1128B DMS 4.1 15.3 + - - -
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Residues in contact with CYS 11 (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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7B GLY 2.7 18.8 + - - +
8B THR 3.5 7.2 - - - +
9B VAL 3.3 0.2 - - - -
10B GLY* 1.3 76.3 - - - +
12B VAL* 1.3 58.5 + - - +
67B TRP* 3.8 15.0 - - + -
69B CYS* 2.0 50.9 - - + -
72B GLN* 3.3 29.6 - - - +
73B SER 3.5 27.8 - - - -
74B VAL* 4.2 2.7 - - - -
1128B DMS 4.0 8.0 - - + -
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Residues in contact with VAL 12 (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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8B THR 3.3 18.4 + - - +
9B VAL 4.3 1.1 - - - +
10B GLY 3.4 0.2 - - - -
11B CYS* 1.3 78.7 - - - +
13B GLY* 1.3 63.1 + - - +
14B PRO* 4.8 0.5 - - - +
72B GLN* 3.5 31.3 - - - +
73B SER* 4.6 0.7 - - - -
74B VAL* 3.8 19.1 - - + +
95B ALA* 3.6 26.0 - - + +
96B ASN* 4.3 13.5 - - - +
99B ALA* 3.4 29.9 - - + +
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Residues in contact with GLY 13 (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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9B VAL* 2.9 18.1 + - - +
10B GLY 3.9 5.1 + - - -
11B CYS 3.6 1.6 - - - -
12B VAL* 1.3 83.3 - - - +
14B PRO* 1.4 72.4 - - - +
15B ARG* 3.5 8.1 - - - -
20B TYR* 5.4 1.7 + - - -
72B GLN* 5.7 1.6 - - - -
95B ALA 4.5 1.0 - - - +
98B LEU* 4.6 1.6 - - - +
99B ALA* 3.3 19.8 + - - +
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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