Contacts of the helix formed by residues 2 - 22 (chain A) in PDB entry 1UHG
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 SER 2 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GLY* 1.3 79.8 + - - +
3A ILE* 1.3 59.7 + - - +
4A GLY* 3.8 3.1 + - - -
5A ALA* 3.2 22.9 + - - +
6A ALA* 3.0 24.1 + - - +
62A LEU* 3.4 11.9 - - - +
63A PRO* 4.9 3.4 - - - -
373A THR 6.0 0.4 - - - -
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Residues in contact with ILE 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SER* 1.3 70.7 - - - +
4A GLY* 1.3 63.0 + - - +
6A ALA* 4.5 0.7 - - + +
7A SER* 2.8 33.6 + - - +
32A ILE* 4.1 21.5 - - + -
35A MET* 4.2 21.5 - - + -
62A LEU* 3.7 17.9 - - + +
63A PRO* 5.3 0.2 - - - +
82A SER* 3.8 27.7 - - - +
83A LEU* 4.4 11.0 - - + -
86A ILE* 3.8 32.8 - - + -
373A THR* 3.8 19.3 - - + +
375A ALA* 4.3 2.5 - - + -
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Residues in contact with GLY 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 3.2 4.7 + - - -
3A ILE* 1.3 86.3 - - - +
5A ALA* 1.3 62.1 + - - +
7A SER* 3.3 2.1 + - - -
8A MET* 3.2 31.4 + - - +
261A PHE* 4.8 0.2 - - - -
373A THR 3.4 24.2 + - - -
374A ASN* 4.0 4.5 - - - -
375A ALA* 3.9 12.8 - - - -
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Residues in contact with ALA 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A GLY 4.9 5.2 - - - +
2A SER* 3.2 24.5 + - - +
4A GLY* 1.3 76.7 - - - +
6A ALA* 1.3 57.8 + - - +
8A MET* 3.8 1.6 - - - +
9A GLU* 3.0 38.9 + - - +
261A PHE* 3.7 34.3 - - + -
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Residues in contact with ALA 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A GLY 5.4 3.1 - - - +
2A SER 3.0 17.9 + - - +
3A ILE 4.2 1.6 - - - +
5A ALA* 1.3 73.1 - - - +
7A SER* 1.3 61.9 + - - +
9A GLU* 3.9 9.6 - - - +
10A PHE* 2.9 31.5 + - - +
35A MET* 3.9 12.9 - - + +
57A VAL 4.7 2.4 - - - +
58A ARG* 3.9 21.2 + - + +
60A ASP* 5.8 0.2 - - - +
62A LEU* 3.8 19.5 - - + -
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Residues in contact with SER 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ILE* 2.8 31.6 + - - -
4A GLY 3.3 3.8 + - - -
6A ALA* 1.3 74.1 - - - +
8A MET* 1.3 59.1 + - - +
10A PHE* 3.8 0.9 - - - +
11A CYS* 2.8 29.3 + - - +
31A PRO* 4.4 5.1 - - - +
32A ILE* 4.5 3.8 - - - -
35A MET* 3.7 24.8 - - - +
375A ALA* 3.3 6.8 - - - -
376A VAL* 3.0 34.8 + - - -
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Residues in contact with MET 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A GLY 3.2 14.5 + - - +
5A ALA 3.8 0.2 - - - +
7A SER* 1.3 77.9 + - - +
9A GLU* 1.3 65.6 + - - +
11A CYS* 3.2 2.1 + - - +
12A PHE* 2.9 39.6 + - + -
261A PHE* 3.3 54.7 - - + +
264A LEU* 3.8 24.9 - - + -
265A THR* 4.6 4.0 - - - +
374A ASN* 3.3 35.0 - - + +
376A VAL* 3.1 27.4 - - + -
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Residues in contact with GLU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ALA* 3.0 26.2 + - - +
6A ALA* 3.9 7.0 - - - +
8A MET* 1.3 76.4 - - - +
10A PHE* 1.3 64.8 + - - +
12A PHE* 3.3 4.0 + - - +
13A ASP* 3.0 26.5 + - - +
58A ARG* 3.5 40.6 + - - +
261A PHE* 4.2 26.6 - - + +
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Residues in contact with PHE 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ALA 2.9 19.6 + - - +
7A SER 3.8 2.2 - - - +
9A GLU* 1.3 75.4 - - - +
11A CYS* 1.3 57.8 + - - +
13A ASP* 3.2 3.2 + - - +
14A VAL* 2.9 51.4 + - + +
31A PRO* 4.1 10.8 - - + -
34A ILE* 3.7 34.8 - - + -
35A MET* 3.5 35.0 - - + -
38A LEU* 4.3 9.4 - - + -
56A VAL* 3.7 24.9 - - + -
57A VAL* 4.0 19.7 - - + +
58A ARG* 3.6 9.8 - - - +
297A LEU* 4.4 7.0 - - + -
300A MET* 3.9 20.4 - - + -
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Residues in contact with CYS 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A SER 2.8 19.7 + - - +
8A MET* 3.4 9.9 - - - +
10A PHE* 1.3 77.3 - - - +
12A PHE* 1.3 63.4 + - + +
14A VAL* 3.3 2.1 + - - +
15A PHE 2.9 13.2 + - - -
29A TYR* 2.7 39.0 + - - -
31A PRO* 3.6 24.2 - - + -
376A VAL* 4.0 9.9 - - + -
379A PHE* 3.4 36.3 - - - -
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Residues in contact with PHE 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A MET* 2.9 39.1 + - + +
9A GLU* 4.1 4.3 - - - +
11A CYS* 1.3 78.8 - - + +
13A ASP* 1.3 61.8 + - - +
15A PHE* 3.3 11.5 + + + +
16A LYS* 2.9 28.6 + - - +
259A ILE* 3.7 42.8 - - + +
260A ASN* 3.5 23.8 - - + -
261A PHE* 3.5 20.9 - - - -
264A LEU* 4.3 12.1 - - + -
379A PHE* 3.7 38.1 - + - -
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Residues in contact with ASP 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLU 3.0 10.9 + - - -
10A PHE 3.2 8.0 + - - +
12A PHE* 1.3 75.6 - - - +
14A VAL* 1.3 65.4 + - - +
16A LYS* 3.3 12.5 + - - +
17A GLU* 3.2 20.8 + - - +
56A VAL 4.7 0.9 - - - +
58A ARG* 2.4 40.8 + - - +
300A MET* 3.5 22.0 - - + +
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Residues in contact with VAL 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A PHE* 2.9 50.4 + - + +
11A CYS 3.6 6.1 - - - +
13A ASP* 1.3 75.5 - - - +
15A PHE* 1.3 64.6 + - - +
17A GLU* 3.2 3.2 + - - +
18A LEU* 3.0 38.6 + - + +
29A TYR* 3.8 26.2 - - + -
34A ILE* 5.1 8.3 - - + -
293A LEU* 6.5 0.2 - - + -
296A VAL* 4.4 11.2 - - + -
297A LEU* 5.6 0.7 - - + -
300A MET* 3.9 18.4 - - + -
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Residues in contact with PHE 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A CYS 2.9 11.6 + - - +
12A PHE* 3.5 16.4 - + - +
13A ASP 3.2 0.2 - - - -
14A VAL* 1.3 77.3 - - - +
16A LYS* 1.3 64.6 + - - +
18A LEU* 3.2 2.7 + - + -
19A LYS* 3.0 47.3 + - + +
27A ILE* 4.0 34.8 - - + -
29A TYR* 3.3 16.5 + - - +
256A GLU* 3.6 45.1 - - + -
259A ILE* 4.9 5.2 - - + -
365A LEU* 4.0 12.6 - - + -
379A PHE* 3.6 34.3 - + + -
381A ARG* 4.5 8.5 - - + -
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Residues in contact with LYS 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A PHE 2.9 14.4 + - - +
13A ASP* 3.3 16.1 + - - +
15A PHE* 1.3 80.0 - - - +
17A GLU* 1.3 61.1 + - - +
19A LYS* 3.5 23.8 - - + +
20A VAL* 3.8 9.7 - - - +
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Residues in contact with GLU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP 3.2 9.9 + - - +
14A VAL 3.8 5.6 - - - +
15A PHE 3.2 0.4 - - - -
16A LYS* 1.3 78.7 - - - +
18A LEU* 1.3 67.4 + - - +
20A VAL* 3.3 24.6 + - - +
21A HIS* 4.0 21.7 + - - +
295A SER 4.9 1.6 - - - +
296A VAL* 4.0 32.5 - - + +
299A ALA* 3.3 31.5 - - + +
300A MET* 4.3 12.1 - - + -
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Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.0 27.4 + - + +
15A PHE* 3.2 3.8 + - - +
17A GLU* 1.3 73.5 - - + +
19A LYS* 1.3 65.4 + - - +
20A VAL 3.1 0.5 + - - -
21A HIS 3.4 0.9 + - - -
22A HIS* 3.0 42.5 + - + +
27A ILE* 3.8 22.9 - - + -
29A TYR* 3.7 33.9 - - + -
291A TYR* 3.7 33.7 - - + -
296A VAL* 3.7 32.1 - - + -
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Residues in contact with LYS 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 3.0 46.0 + - + +
16A LYS* 3.5 16.8 - - - +
18A LEU* 1.3 78.4 - - - +
20A VAL* 1.3 62.4 + - - +
22A HIS* 3.8 6.0 + - - +
23A ALA* 3.9 13.5 + - - +
27A ILE* 4.6 1.8 - - + +
253A GLU* 5.2 7.5 + - - +
256A GLU* 2.9 39.8 + - + +
257A SER* 5.7 1.8 - - - +
381A ARG* 3.8 21.1 + - - +
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Residues in contact with VAL 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS 3.8 11.4 - - - +
17A GLU* 3.4 28.3 - - - +
18A LEU 3.1 0.4 - - - -
19A LYS* 1.3 78.7 - - - +
21A HIS* 1.3 88.2 + - + +
22A HIS 3.8 0.3 + - - -
23A ALA* 4.8 4.3 + - - +
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Residues in contact with HIS 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU* 4.0 15.2 + - - -
18A LEU 3.4 3.6 + - - -
20A VAL* 1.3 100.0 + - + +
22A HIS* 1.3 77.3 + - + +
23A ALA 3.8 1.8 - - - -
25A GLU* 5.0 2.1 - - - +
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Residues in contact with HIS 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.0 36.5 + - + +
19A LYS 4.3 3.4 - - - -
20A VAL 3.5 0.8 - - - -
21A HIS* 1.3 92.9 + - + +
23A ALA* 1.3 67.1 + - - +
25A GLU* 3.4 29.5 + - + +
26A ASN 5.3 2.2 + - - +
27A ILE* 4.2 15.5 - - + -
289A GLU* 6.1 0.9 - - - -
290A LYS 5.5 2.2 - - - -
291A TYR* 3.7 36.2 - + - -
381A ARG* 3.0 17.9 + - - -
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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