Contacts of the helix formed by residues 5 - 21 (chain A) in PDB entry 4U2M
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 GLN 5 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PHE 3.2 0.8 - - - -
4A PRO* 1.3 90.1 - - + +
6A HIS* 1.3 65.3 + - - +
7A SER 3.3 2.5 - - - -
8A GLN* 3.2 13.8 + - + +
9A HIS* 2.9 23.2 + - + +
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Residues in contact with HIS 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PHE* 3.1 28.7 + - + +
4A PRO 3.4 0.2 - - - -
5A GLN* 1.3 78.4 - - - +
7A SER* 1.3 58.7 + - - +
9A HIS* 3.2 15.9 + + - +
10A VAL* 2.9 44.4 + - + +
142A LEU* 3.9 7.2 - - + -
176A CYS* 3.7 17.0 - - + -
212A PHE* 3.6 29.6 + + + -
213A MET* 2.8 26.3 + - - -
216A SER* 3.1 29.4 - - - +
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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
----------------------------------------------------------
4A PRO 4.9 5.8 + - - -
5A GLN 3.3 0.4 - - - -
6A HIS* 1.3 79.3 - - - +
8A GLN* 1.3 58.7 + - - +
10A VAL* 3.4 4.0 + - - +
11A LEU* 3.0 23.2 + - - +
138A ALA* 3.6 28.8 - - - +
139A SER* 3.0 29.2 + - - -
142A LEU* 3.8 26.1 - - - +
216A SER* 3.9 5.7 + - - -
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Residues in contact with GLN 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO 5.5 0.6 + - - +
5A GLN* 3.2 16.0 + - + +
7A SER* 1.3 78.1 + - - +
9A HIS* 1.3 66.6 + - - +
11A LEU* 3.4 12.0 + - - +
12A GLU* 3.0 30.1 + - + +
79A THR 5.5 3.4 + - - -
135A THR 5.7 0.5 - - - +
138A ALA* 3.6 19.9 - - + +
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Residues in contact with HIS 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLN* 2.9 13.2 + - + +
6A HIS* 3.4 22.0 - + - +
8A GLN* 1.3 79.1 - - - +
10A VAL* 1.3 65.0 + - + +
12A GLU* 3.4 6.9 + - - +
13A GLN* 3.0 57.8 + - + +
175A ALA 4.1 10.6 + - - -
176A CYS* 5.7 2.2 - - - -
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Residues in contact with VAL 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A HIS* 2.9 47.2 + - + +
7A SER* 3.7 9.2 - - - +
9A HIS* 1.3 78.9 - - + +
11A LEU* 1.3 64.1 + - - +
13A GLN* 3.1 9.0 + - - +
14A LEU* 2.8 41.3 + - + +
141A VAL* 6.3 0.2 - - + -
142A LEU* 4.1 23.1 - - + -
145A LEU* 5.2 3.1 - - + -
172A VAL* 5.4 5.4 - - + -
175A ALA* 4.4 10.1 - - + -
176A CYS* 3.9 15.0 - - - -
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Residues in contact with LEU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A SER 3.0 16.8 + - - +
8A GLN* 3.7 13.9 - - - +
9A HIS 3.4 0.2 - - - -
10A VAL* 1.3 78.4 - - - +
12A GLU* 1.3 57.0 + - - +
14A LEU* 3.2 14.0 + - + +
15A ASN* 2.9 27.7 + - - +
41A VAL* 5.8 1.3 - - + -
77A MET 3.5 21.5 - - - +
78A TYR* 3.4 20.7 - - + +
79A THR* 4.1 19.3 - - - +
80A ALA* 4.4 4.3 - - + -
137A HIS* 4.1 11.2 - - + -
138A ALA* 3.9 21.8 - - + +
141A VAL* 4.4 24.7 - - + -
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Residues in contact with GLU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLN* 3.0 26.3 + - - +
9A HIS* 3.8 6.3 - - - +
11A LEU* 1.3 77.6 - - - +
13A GLN* 1.3 60.7 + - - +
15A ASN* 3.2 7.2 + - - +
16A GLN* 2.9 28.9 + - - +
78A TYR 5.3 0.2 - - - -
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Residues in contact with GLN 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A HIS* 3.0 42.1 + - + +
10A VAL 3.1 6.5 + - - +
12A GLU* 1.3 79.9 - - - +
14A LEU* 1.3 57.6 + - - +
16A GLN* 3.4 23.4 + - - +
17A GLN* 2.9 35.1 + - - +
174A MET 4.6 2.6 - - - +
175A ALA* 3.5 40.9 - - + +
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Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 2.8 36.4 + - + +
11A LEU* 3.5 15.9 - - + +
13A GLN* 1.3 72.3 - - - +
15A ASN* 1.3 58.3 + - - +
17A GLN* 3.3 8.1 + - - +
18A ARG 3.0 22.5 + - - -
38A HIS* 3.7 1.5 - - + -
41A VAL* 3.9 21.1 - - + -
78A TYR* 3.5 22.8 - - + -
141A VAL* 4.6 9.6 - - + -
145A LEU* 4.3 14.4 - - + -
171A THR* 3.1 47.6 - - + +
172A VAL* 4.8 2.7 - - + +
175A ALA* 4.6 4.0 - - + -
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Residues in contact with ASN 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU 2.9 8.2 + - - +
12A GLU* 3.6 10.7 - - - +
13A GLN 3.2 0.2 - - - -
14A LEU* 1.3 75.8 - - - +
16A GLN* 1.3 64.9 + - - +
18A ARG* 3.0 31.9 + - - +
19A GLN* 3.0 44.4 + - - +
75A GLU* 5.3 0.6 + - - -
78A TYR* 3.5 29.2 + - + +
79A THR* 3.6 20.3 - - - +
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Residues in contact with GLN 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU 2.9 15.6 + - - +
13A GLN* 3.6 29.3 + - - +
15A ASN* 1.3 79.0 - - - +
17A GLN* 1.3 63.2 + - - +
19A GLN* 3.3 10.7 + - + +
20A LEU* 3.1 41.8 + - + +
22A LEU* 6.2 0.4 - - + -
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Residues in contact with GLN 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLN* 2.9 21.7 + - - +
14A LEU* 3.5 9.9 - - - +
16A GLN* 1.3 76.8 - - - +
18A ARG* 1.3 58.3 + - - +
20A LEU 3.0 2.4 + - - -
21A GLY 2.8 24.9 + - - -
22A LEU* 2.9 35.8 + - + +
23A LEU* 3.9 3.6 - - - +
38A HIS* 3.1 10.6 + - - +
171A THR* 2.5 48.9 + - - -
174A MET* 3.7 26.6 - - + +
175A ALA* 3.6 20.6 - - - +
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Residues in contact with ARG 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU 3.0 13.6 + - - +
15A ASN* 3.0 28.9 + - - +
17A GLN* 1.3 75.5 - - - +
19A GLN* 1.3 72.6 + - - +
21A GLY* 3.1 11.4 + - - -
24A CYS* 3.8 13.0 - - - -
35A PHE* 5.2 7.9 - - - +
36A LYS* 3.3 34.4 + - - +
37A ALA* 5.2 0.2 - - - -
38A HIS* 3.9 1.9 - - + -
71A GLY 5.4 0.4 + - - -
74A LEU* 4.1 25.1 - - - +
75A GLU* 3.0 35.0 + - - +
78A TYR* 3.5 44.1 - - + +
79A THR* 4.7 0.4 - - - +
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Residues in contact with GLN 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASN* 3.0 46.9 + - - +
16A GLN* 3.7 9.2 - - + +
18A ARG* 1.3 86.5 - - - +
20A LEU* 1.3 66.2 + - + +
21A GLY 3.7 0.2 + - - -
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Residues in contact with LEU 20 (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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16A GLN* 3.1 36.3 + - + +
17A GLN 3.0 5.0 + - - +
19A GLN* 1.3 83.3 - - + +
21A GLY* 1.3 62.6 + - - +
22A LEU* 3.3 26.1 + - + -
31C ASP* 3.7 12.5 + - - -
32C GLY* 3.8 8.1 + - - +
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Residues in contact with GLY 21 (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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17A GLN 2.8 6.6 + - - -
18A ARG 3.1 8.9 + - - -
19A GLN 3.4 0.8 + - - -
20A LEU* 1.3 77.7 - - - +
22A LEU* 1.3 62.3 + - - -
23A LEU 3.3 1.0 + - - -
24A CYS* 3.4 12.8 + - - +
36A LYS* 3.5 29.1 - - - +
31C ASP* 3.0 28.5 - - - +
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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