Contacts of the helix formed by residues 5 - 21 (chain B) in PDB entry 1UMD
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 THR 5 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B MET* 1.3 75.4 - - - +
6B MET* 1.3 65.8 + - - +
7B VAL* 3.6 6.2 + - - +
8B GLN* 2.8 34.2 + - - +
9B ALA* 3.0 21.5 + - - +
151B PRO* 3.8 2.5 - - - -
177B TYR 3.5 11.3 + - - -
178B ARG* 4.0 25.6 - - + +
180B VAL 3.5 9.0 - - - +
181B LYS* 3.8 29.4 - - + +
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Residues in contact with MET 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B THR* 1.3 73.8 - - - +
7B VAL* 1.3 58.2 + - - +
9B ALA* 3.1 2.4 + - - +
10B LEU* 2.8 50.5 + - + +
148B VAL* 4.0 19.1 - - + +
149B SER* 3.7 36.8 - - - +
150B THR* 3.7 10.5 - - - +
151B PRO* 3.6 20.1 - - + +
154B ALA* 3.8 10.1 - - + -
172B GLU* 4.7 5.2 - - - -
173B PRO* 4.4 7.6 - - - +
176B LEU* 3.5 28.2 + - + +
177B TYR* 3.2 26.2 + - + +
180B VAL 4.4 1.2 + - - -
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Residues in contact with VAL 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B THR* 3.2 4.9 - - - +
6B MET* 1.3 77.1 - - - +
8B GLN* 1.3 60.8 + - + +
10B LEU* 3.3 8.8 + - - +
11B ASN* 2.9 29.4 + - + +
38B PHE 3.4 25.8 - - - +
39B LEU* 3.7 23.6 - - + +
40B VAL* 4.0 4.9 - - - +
177B TYR* 3.1 45.8 + - + +
178B ARG* 4.1 11.4 - - + -
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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
----------------------------------------------------------
3B LEU 4.2 1.0 - - - +
4B MET* 3.1 28.8 - - + +
5B THR* 2.8 36.3 + - - +
7B VAL* 1.3 79.3 - - + +
9B ALA* 1.3 58.2 + - - +
11B ASN* 3.4 7.5 + - - +
12B ARG* 2.9 30.0 + - - +
181B LYS* 3.1 15.3 + - - +
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Residues in contact with ALA 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B MET* 3.8 17.2 - - - -
5B THR 3.0 17.0 + - - +
6B MET 3.5 4.3 - - - +
8B GLN* 1.3 74.5 - - - +
10B LEU* 1.3 58.7 + - - +
12B ARG* 3.3 3.5 + - - +
13B ALA* 3.0 22.3 + - - +
151B PRO* 3.1 33.7 - - + +
154B ALA* 4.3 0.7 - - + -
155B LYS* 3.6 21.6 - - + +
184B VAL* 4.4 2.2 - - + -
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Residues in contact with LEU 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B MET* 2.8 28.7 + - + +
7B VAL 3.7 3.6 - - - +
9B ALA* 1.3 72.8 - - - +
11B ASN* 1.3 66.6 + - - +
13B ALA* 3.2 4.6 + - - +
14B LEU* 3.0 28.5 + - - +
40B VAL* 3.9 17.0 - - + -
154B ALA* 3.7 24.7 - - + +
158B LEU* 3.7 15.4 - - + +
170B PHE* 3.7 18.2 - - + -
172B GLU* 3.5 40.8 - - + +
177B TYR* 3.7 19.3 - - + -
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Residues in contact with ASN 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 2.9 18.1 + - + +
8B GLN* 3.6 7.6 - - - +
10B LEU* 1.3 76.4 - - - +
12B ARG* 1.3 59.5 + - - +
14B LEU* 3.4 4.6 + - - +
15B ASP* 3.0 32.1 + - - +
39B LEU 4.1 3.4 + - - +
40B VAL* 2.9 31.1 + - - +
41B THR* 3.7 2.6 - - - +
42B GLU* 2.9 36.2 + - - +
44B LEU* 4.4 7.9 - - - +
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Residues in contact with ARG 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B MET* 4.7 9.4 - - + -
8B GLN 2.9 17.7 + - - +
9B ALA* 3.5 8.3 - - - +
11B ASN* 1.3 77.5 + - - +
13B ALA* 1.3 60.6 + - - +
15B ASP* 3.3 9.9 + - - +
16B GLU* 2.6 65.0 + - - +
155B LYS* 4.1 12.3 - - + +
186B GLU* 3.1 49.8 + - - +
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Residues in contact with ALA 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA 3.0 13.6 + - - +
10B LEU 3.4 8.7 - - - +
12B ARG* 1.3 77.9 - - - +
14B LEU* 1.3 62.8 + - - +
16B GLU* 3.4 2.3 + - - +
17B GLU* 3.0 30.4 + - - +
155B LYS* 3.7 17.7 - - - +
158B LEU* 4.0 16.2 - - + -
159B LYS* 3.7 28.7 - - + +
162B ILE* 5.1 0.9 - - - -
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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 LEU 3.0 18.8 + - - +
11B ASN 3.7 5.4 - - - +
13B ALA* 1.3 75.0 - - - +
15B ASP* 1.3 66.4 + - - +
17B GLU* 3.4 3.0 + - - +
18B MET* 2.9 33.8 + - - +
24B VAL* 5.9 1.8 - - + -
26B VAL* 4.6 7.2 - - + -
40B VAL* 4.0 28.5 - - + +
41B THR* 4.0 19.7 - - + -
44B LEU* 3.8 15.5 - - + -
78B VAL* 4.0 27.1 - - + -
116B ARG* 4.6 6.5 - - - +
158B LEU* 3.9 19.5 - - + -
162B ILE* 4.1 12.1 - - + -
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Residues in contact with ASP 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ASN* 3.0 22.5 + - - +
12B ARG* 3.3 12.0 + - - +
14B LEU* 1.3 77.4 - - - +
16B GLU* 1.3 58.7 + - + +
18B MET* 3.7 0.3 - - - +
19B ALA* 2.9 15.8 + - - +
44B LEU* 3.9 16.7 - - + +
47B LYS* 2.8 30.1 + - - +
48B TYR* 2.6 45.0 + - - -
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Residues in contact with GLU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ARG* 2.6 58.9 + - - +
13B ALA 3.7 1.1 - - - +
15B ASP* 1.3 76.2 - - + +
17B GLU* 1.3 63.6 + - - +
19B ALA* 3.2 7.3 + - - +
20B LYS* 3.0 30.1 + - - +
155B LYS* 2.8 33.2 + - - -
159B LYS* 2.8 30.6 + - - +
186B GLU 3.0 8.6 - - - +
187B GLU 4.9 0.7 - - - -
188B ASP* 4.1 7.3 - - - +
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Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA 3.0 20.7 + - - +
14B LEU 4.0 1.6 - - - +
16B GLU* 1.3 75.7 - - - +
18B MET* 1.3 57.8 + - - +
20B LYS* 3.3 9.4 + - - +
21B ASP* 2.9 28.9 + - - +
24B VAL* 3.8 9.6 - - + +
159B LYS* 2.7 42.4 + - + -
162B ILE* 3.6 41.1 - - + +
163B ARG* 2.9 40.6 + - - +
188B ASP* 4.0 0.2 - - - +
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Residues in contact with MET 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 2.9 22.2 + - + +
15B ASP 3.7 3.4 - - - +
17B GLU* 1.3 73.9 - - - +
19B ALA* 1.3 65.0 + - - +
21B ASP 3.3 7.7 + - - +
22B PRO 4.3 0.2 - - - -
24B VAL* 3.6 32.3 - - + +
25B VAL* 4.5 1.3 - - - -
26B VAL* 4.0 18.8 - - - -
44B LEU* 4.2 14.6 - - - -
48B TYR* 3.8 36.1 - - + -
52B ARG* 3.0 70.2 + - + +
53B VAL* 4.0 5.2 - - + -
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ASP* 2.9 13.8 + - - +
16B GLU* 3.2 8.5 + - - +
18B MET* 1.3 77.7 - - - +
20B LYS* 1.3 62.2 + - + +
21B ASP 5.2 0.2 - - - -
22B PRO* 5.5 1.0 - - - +
47B LYS* 5.2 3.8 - - - +
48B TYR* 3.3 22.1 + - + +
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Residues in contact with LYS 20 (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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16B GLU* 3.0 21.2 + - - +
17B GLU* 3.7 11.4 - - - +
18B MET 3.2 0.4 - - - -
19B ALA* 1.3 79.7 - - + +
21B ASP* 1.3 59.9 + - + +
22B PRO* 4.1 5.1 - - - +
163B ARG* 3.8 17.0 - - - +
188B ASP* 3.0 38.0 - - - +
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Residues in contact with ASP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLU* 2.9 13.4 + - - +
18B MET 3.3 5.1 - - - +
20B LYS* 1.3 80.7 - - + +
22B PRO* 1.3 68.8 - - - +
23B ARG* 2.6 60.6 + - - +
24B VAL* 3.1 17.9 + - + +
52B ARG* 2.9 17.0 + - - -
76B ARG* 3.3 9.9 + - - -
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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