Contacts of the helix formed by residues 5 - 21 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ASP* 4.8 4.9 - - - +
165A GLN* 5.0 1.2 + - - +
167A ARG* 3.2 47.7 + - - +
3B PHE 3.1 1.2 + - - -
4B PRO* 1.3 98.9 - - + +
6B HIS* 1.3 64.5 + - - +
7B SER 3.4 1.8 - - - -
8B GLN* 3.2 30.4 + - - +
9B HIS* 3.0 46.2 + - + +
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Residues in contact with HIS 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B PHE* 3.1 29.0 + - + +
4B PRO 3.4 0.8 - - - -
5B GLN* 1.3 77.6 - - - +
7B SER* 1.3 64.0 + - - +
9B HIS* 3.1 12.5 + - + +
10B VAL* 3.0 41.4 + - + +
142B LEU* 3.8 7.6 - - + -
176B CYS* 3.8 16.6 - - + -
212B PHE* 3.6 29.0 + + + -
213B MET* 2.8 28.7 + - - -
216B SER* 3.1 30.5 - - - +
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Residues in contact with SER 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B PHE 4.8 0.2 + - - -
4B PRO 4.8 6.8 + - - -
6B HIS* 1.3 80.3 - - - +
8B GLN* 1.3 57.4 + - - +
10B VAL* 3.4 3.9 + - - +
11B LEU* 3.0 23.6 + - - +
138B ALA* 3.6 30.4 - - - +
139B SER* 3.0 31.0 + - - -
142B LEU* 3.9 23.7 - - - +
216B SER* 3.9 5.4 + - - -
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Residues in contact with GLN 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PRO 5.5 0.6 + - - +
5B GLN* 3.2 31.1 + - - +
6B HIS 3.2 0.4 - - - -
7B SER* 1.3 77.8 + - - +
9B HIS* 1.3 68.6 + - + +
11B LEU* 3.4 11.8 + - - +
12B GLU* 3.0 60.5 + - - +
79B THR* 5.1 5.7 + - - +
80B ALA* 5.3 5.0 - - - +
138B ALA* 3.6 21.4 - - + +
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Residues in contact with HIS 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B GLN* 3.0 39.1 + - + +
6B HIS* 3.5 15.0 + - - +
8B GLN* 1.3 78.9 - - + +
10B VAL* 1.3 64.3 + - + +
12B GLU* 3.4 21.4 + - - +
13B GLN* 3.0 30.9 + - + +
239B HIS* 5.0 18.9 - + - -
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Residues in contact with VAL 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B HIS* 3.0 45.9 + - + +
7B SER* 3.6 9.0 - - - +
9B HIS* 1.3 76.8 - - + +
11B LEU* 1.3 59.0 + - - +
13B GLN* 3.1 8.5 + - - +
14B LEU* 2.8 46.9 + - + +
141B VAL* 6.3 0.4 - - + -
142B LEU* 4.1 23.1 - - + -
145B LEU* 5.2 2.7 - - + -
172B VAL* 5.3 5.2 - - + -
175B ALA* 4.3 11.2 - - + +
176B CYS* 3.8 16.4 - - - -
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Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B SER 3.0 17.6 + - - +
8B GLN* 3.7 13.0 - - - +
10B VAL* 1.3 77.9 - - - +
12B GLU* 1.3 61.8 + - - +
14B LEU* 3.2 13.9 + - + +
15B ASN* 2.9 22.7 + - - +
41B VAL* 5.7 1.6 - - + -
77B MET 3.5 20.6 - - - +
78B TYR* 3.4 21.6 - - + +
79B THR* 3.9 22.2 - - - +
80B ALA* 4.3 2.5 - - + -
137B HIS* 4.1 10.5 - - + -
138B ALA* 3.9 20.6 - - + -
141B VAL* 4.5 25.6 - - + -
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Residues in contact with GLU 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLN* 3.0 51.2 + - - +
9B HIS* 3.7 20.3 - - - +
11B LEU* 1.3 76.5 - - - +
13B GLN* 1.3 62.5 + - - +
15B ASN* 3.3 7.6 + - - +
16B GLN* 2.9 31.3 + - + +
78B TYR 5.2 0.4 - - - -
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Residues in contact with GLN 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B HIS* 3.0 21.6 + - + +
10B VAL 3.5 7.0 - - - +
12B GLU* 1.3 79.7 - - - +
14B LEU* 1.3 59.9 + - - +
16B GLN* 3.3 17.1 + - - +
17B GLN* 2.9 35.1 + - - +
174B MET 4.9 3.4 + - - -
175B ALA* 3.4 39.7 + - + +
181B TYR* 5.6 9.1 - - - -
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Residues in contact with LEU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 2.8 34.3 + - + +
11B LEU* 3.2 16.4 + - + +
13B GLN* 1.3 75.7 - - - +
15B ASN* 1.3 57.8 + - - +
17B GLN* 3.4 9.0 + - - +
18B ARG 3.0 22.7 + - - -
38B HIS* 3.7 1.2 - - - -
41B VAL* 3.9 20.4 - - + -
78B TYR* 3.5 23.8 - - + -
141B VAL* 4.6 9.9 - - + -
145B LEU* 4.3 14.4 - - + -
171B THR* 2.9 48.0 - - + +
172B VAL* 4.7 4.5 - - + +
175B ALA* 4.5 4.3 - - + -
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Residues in contact with ASN 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU 2.9 7.2 + - - +
12B GLU* 3.6 10.5 - - - +
14B LEU* 1.3 76.4 - - - +
16B GLN* 1.3 65.5 + - - +
18B ARG* 3.0 32.9 + - - +
19B GLN* 3.0 44.3 + - - +
75B GLU* 5.1 1.4 + - - -
78B TYR* 3.5 29.1 - - - +
79B THR* 3.7 17.9 - - - +
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Residues in contact with GLN 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLU* 2.9 17.6 + - + +
13B GLN* 3.5 23.6 - - - +
15B ASN* 1.3 74.7 - - - +
17B GLN* 1.3 66.2 + - + +
19B GLN* 3.3 23.4 + - - +
20B LEU* 3.1 37.4 + - + +
22B LEU* 5.6 0.2 - - - -
16D GLN* 3.9 15.0 + - - +
19D GLN* 3.7 18.8 + - - +
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Residues in contact with GLN 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLN* 2.9 21.0 + - - +
14B LEU* 3.5 9.3 - - - +
16B GLN* 1.3 76.9 - - + +
18B ARG* 1.3 58.2 + - - +
20B LEU 3.1 2.3 + - - -
21B GLY 2.8 24.3 + - - -
22B LEU* 2.9 35.5 + - + +
23B LEU* 3.9 2.6 - - - +
38B HIS* 3.1 8.1 + - - +
171B THR* 2.9 54.0 + - - +
174B MET* 3.7 35.4 - - + +
175B ALA* 3.7 11.5 - - - +
181B TYR* 5.7 1.8 - - + -
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Residues in contact with ARG 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU 3.0 14.5 + - - +
15B ASN* 3.0 30.7 + - - +
17B GLN* 1.3 76.2 - - - +
19B GLN* 1.3 70.0 + - - +
21B GLY* 3.1 11.6 + - - -
24B CYS* 3.8 12.7 - - - -
35B PHE* 5.2 8.1 - - - -
36B LYS* 3.4 35.0 + - + +
38B HIS* 3.9 2.7 - - + -
71B GLY 5.3 0.8 + - - -
74B LEU* 4.0 25.1 - - - +
75B GLU* 3.0 34.8 + - - +
78B TYR* 3.5 42.9 - - + +
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Residues in contact with GLN 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASN* 3.0 43.2 + - - +
16B GLN* 3.7 20.4 + - - +
18B ARG* 1.3 83.3 - - + +
20B LEU* 1.3 61.2 + - - +
16D GLN* 3.4 19.7 + - - +
19D GLN* 3.4 42.5 - - + +
20D LEU* 3.6 33.0 - - + +
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Residues in contact with LEU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLN* 3.1 26.4 + - + +
17B GLN 3.1 4.9 + - - +
19B GLN* 1.3 76.1 - - - +
21B GLY* 1.3 59.3 + - - +
22B LEU* 3.2 33.2 + - + +
181B TYR* 4.5 8.3 - - - +
19D GLN* 3.5 42.2 - - + +
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Residues in contact with GLY 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLN 2.8 4.9 + - - -
18B ARG 3.1 11.4 + - - -
19B GLN 3.4 0.8 + - - -
20B LEU* 1.3 77.0 - - - +
22B LEU* 1.3 64.0 + - - +
23B LEU 3.4 2.8 + - - -
24B CYS* 3.4 17.5 + - - +
36B LYS* 3.9 31.0 - - - +
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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