Contacts of the helix formed by residues 5 - 21 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199A PRO* 6.1 6.7 - - + -
3D PHE 3.2 0.8 - - - -
4D PRO* 1.3 101.3 - - + +
6D HIS* 1.3 65.5 + - - +
7D SER 3.3 2.7 - - - -
8D GLN* 3.2 31.0 + - - +
9D HIS* 3.0 45.6 + - + +
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Residues in contact with HIS 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D PHE* 3.1 28.7 + - + +
4D PRO 3.4 0.4 - - - -
5D GLN* 1.3 78.5 - - - +
7D SER* 1.3 57.7 + - - +
9D HIS* 3.1 12.9 + - - +
10D VAL* 2.9 45.8 + - + +
142D LEU* 3.8 6.3 - - + -
176D CYS* 3.8 17.3 - - + -
212D PHE* 3.6 28.1 + + + -
213D MET* 2.9 28.9 + - - -
216D SER* 3.1 31.4 - - - +
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Residues in contact with SER 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D PRO 4.8 6.5 + - - -
5D GLN 3.3 0.8 - - - -
6D HIS* 1.3 78.3 - - - +
8D GLN* 1.3 59.1 + - - +
10D VAL* 3.6 3.8 - - - +
11D LEU* 3.0 27.7 + - - +
138D ALA* 3.6 26.5 - - - +
139D SER* 3.0 28.2 + - - -
142D LEU* 3.8 25.1 - - - +
216D SER* 4.0 5.1 + - - -
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Residues in contact with GLN 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D PRO 5.6 0.4 - - - +
5D GLN* 3.2 30.6 + - - +
6D HIS 3.2 0.4 - - - -
7D SER* 1.3 79.3 + - - +
9D HIS* 1.3 66.9 + - + +
11D LEU* 3.3 12.0 + - - +
12D GLU* 3.0 56.9 + - - +
79D THR 5.2 5.8 + - - +
80D ALA* 5.5 3.3 - - - +
138D ALA* 3.7 20.3 - - + +
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Residues in contact with HIS 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D GLN* 3.0 38.3 + - + +
6D HIS* 3.5 14.3 + - + +
8D GLN* 1.3 81.1 - - + +
10D VAL* 1.3 61.7 + - + +
12D GLU* 3.4 20.6 + - - +
13D GLN* 3.0 30.4 + - + +
239D HIS* 5.2 16.8 - + - -
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Residues in contact with VAL 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D HIS* 2.9 46.1 + - + +
7D SER* 3.6 9.2 - - - +
9D HIS* 1.3 76.9 - - + +
11D LEU* 1.3 64.5 + - - +
13D GLN* 3.1 8.7 + - - +
14D LEU* 2.9 40.5 + - + +
141D VAL* 6.3 0.9 - - + -
142D LEU* 4.1 22.4 - - + -
145D LEU* 5.1 3.4 - - + -
172D VAL* 5.3 5.4 - - + -
175D ALA* 4.3 10.8 - - + +
176D CYS* 3.8 15.9 - - - -
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Residues in contact with LEU 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D SER 3.0 16.6 + - - +
8D GLN* 3.7 13.5 - - - +
10D VAL* 1.3 76.1 - - - +
12D GLU* 1.3 63.2 + - - +
14D LEU* 3.2 15.1 + - + +
15D ASN* 3.0 22.3 + - - +
41D VAL* 5.7 1.3 - - + -
77D MET 3.5 21.3 - - - +
78D TYR* 3.4 22.1 - - + +
79D THR* 3.9 22.9 - - - +
80D ALA* 4.4 2.7 - - + -
137D HIS* 4.1 10.1 - - + -
138D ALA* 3.9 21.5 - - + +
141D VAL* 4.4 25.8 - - + -
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Residues in contact with GLU 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D GLN* 3.0 50.0 + - - +
9D HIS* 3.7 22.7 - - - +
11D LEU* 1.3 75.2 - - - +
13D GLN* 1.3 62.1 + - - +
15D ASN* 3.3 8.3 + - - +
16D GLN* 2.9 32.5 + - + +
78D TYR 5.2 0.9 - - - -
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Residues in contact with GLN 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D HIS* 3.0 21.5 + - + +
10D VAL 3.1 6.9 + - - +
12D GLU* 1.3 80.8 - - - +
14D LEU* 1.3 57.1 + - - +
16D GLN* 3.3 16.7 + - - +
17D GLN* 2.9 34.4 + - - +
174D MET 4.8 3.4 + - - -
175D ALA* 3.4 41.1 + - + +
181D TYR* 5.4 10.3 - - - -
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Residues in contact with LEU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D VAL* 2.9 33.1 + - + +
11D LEU* 3.2 17.0 + - + +
13D GLN* 1.3 76.8 - - - +
15D ASN* 1.3 59.0 + - - +
17D GLN* 3.3 8.0 + - - +
18D ARG 3.0 22.2 + - - -
38D HIS* 3.7 1.4 - - + -
41D VAL* 3.8 20.4 - - + -
78D TYR* 3.5 23.6 - - + -
141D VAL* 4.6 9.6 - - + -
145D LEU* 4.3 14.1 - - + -
171D THR* 3.1 46.2 - - + +
172D VAL* 4.7 2.9 - - + +
175D ALA* 4.5 4.5 - - + -
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Residues in contact with ASN 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LEU 3.0 7.0 + - - +
12D GLU* 3.6 11.1 - - - +
14D LEU* 1.3 75.7 - - - +
16D GLN* 1.3 66.3 + - - +
18D ARG* 3.0 32.3 + - - +
19D GLN* 3.0 44.9 + - - +
75D GLU* 5.0 1.6 + - - -
78D TYR* 3.5 30.5 - - - +
79D THR* 3.7 18.0 - - - +
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Residues in contact with GLN 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLN* 3.9 15.8 + - - +
19B GLN* 3.4 20.6 + - - +
12D GLU* 2.9 18.6 + - + +
13D GLN* 3.5 23.1 - - - +
15D ASN* 1.3 77.6 - - - +
17D GLN* 1.3 64.5 + - + +
19D GLN* 3.3 23.4 + - - +
20D LEU* 3.1 36.9 + - + +
22D LEU* 5.6 0.2 - - - -
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Residues in contact with GLN 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D GLN* 2.9 20.7 + - - +
14D LEU* 3.5 10.3 - - - +
15D ASN 3.3 0.2 - - - -
16D GLN* 1.3 76.9 - - + +
18D ARG* 1.3 57.2 + - - +
20D LEU 3.1 1.9 + - - -
21D GLY 2.9 25.3 + - - -
22D LEU* 3.0 35.7 + - + +
23D LEU* 3.9 3.5 - - - +
38D HIS* 3.1 9.9 + - - +
171D THR* 2.5 50.2 + - - -
174D MET* 3.7 28.0 - - + +
175D ALA* 3.6 19.2 - - - +
181D TYR* 5.7 2.0 - - + -
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Residues in contact with ARG 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LEU 3.0 14.0 + - - +
15D ASN* 3.0 29.9 + - - +
17D GLN* 1.3 76.4 - - - +
19D GLN* 1.3 71.6 + - - +
21D GLY* 3.1 11.4 + - - -
24D CYS* 3.8 12.5 - - - -
35D PHE* 5.7 4.6 - - - -
36D LYS* 3.4 34.8 + - + +
38D HIS* 3.9 2.6 - - + -
71D GLY* 5.1 1.8 + - - -
74D LEU* 4.0 25.4 - - - +
75D GLU* 3.0 34.8 + - - +
78D TYR* 3.6 41.6 - - + +
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Residues in contact with GLN 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLN* 3.7 17.4 + - - +
19B GLN* 3.4 43.1 - - - +
20B LEU* 3.5 34.8 - - + +
15D ASN* 3.0 43.9 + - - +
16D GLN* 3.3 16.6 + - - +
18D ARG* 1.3 84.3 - - - +
20D LEU* 1.3 61.6 + - - +
21D GLY 3.7 0.3 + - - -
75D GLU* 5.8 0.8 + - - -
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Residues in contact with LEU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLN* 3.6 39.9 - - + +
16D GLN* 3.1 26.2 + - + +
17D GLN 3.1 4.4 + - - +
19D GLN* 1.3 78.3 - - - +
21D GLY* 1.3 60.0 + - - +
22D LEU* 3.2 33.6 + - + +
181D TYR* 4.5 8.7 - - - +
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Residues in contact with GLY 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D GLN 2.9 5.6 + - - -
18D ARG 3.1 10.9 + - - -
19D GLN 3.3 0.6 - - - -
20D LEU* 1.3 77.7 - - - +
22D LEU* 1.3 64.5 + - - +
23D LEU 3.4 1.9 + - - -
24D CYS* 3.5 17.1 + - - +
36D LYS* 3.9 30.7 - - - +
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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