Contacts of the helix formed by residues 15 - 29 (chain B) in PDB entry 2R1U
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 GLU 15 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ASP* 2.5 24.7 - - - +
28A ARG* 3.0 29.5 + - - +
13B GLY 3.7 0.8 + - - -
14B ALA* 1.3 69.8 - - - +
16B GLU* 1.3 61.8 + - - +
17B MET* 2.8 42.4 + - - +
18B GLU* 3.1 43.4 + - - +
19B THR* 3.0 15.7 + - - -
47B SER* 3.5 15.4 + - - +
48B ARG* 3.8 4.5 + - - +
73B PRO* 4.6 0.2 - - - +
74B GLY 3.0 9.9 + - - +
75B GLY* 3.8 12.1 - - - +
106B CYS* 5.8 1.3 - - - -
158B PRO* 4.4 2.7 - - + -
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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
----------------------------------------------------------
20A VAL* 3.7 19.5 - - + -
24A ASP* 3.4 20.6 - - - +
14B ALA 3.2 3.0 + - - -
15B GLU* 1.3 72.1 + - - +
17B MET* 1.3 56.7 + - - +
19B THR* 3.6 7.3 - - - -
20B VAL* 2.9 34.0 + - - +
46B CYS* 3.4 22.0 - - + +
47B SER* 2.8 25.8 + - - -
48B ARG* 2.9 27.4 + - - +
50B VAL* 3.1 37.8 + - + +
52B ILE* 4.5 3.8 - - + -
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Residues in contact with MET 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 4.1 7.9 - - + -
21A ILE* 3.9 25.8 - - + +
24A ASP* 3.3 47.3 - - + +
25A VAL* 4.2 3.4 - - + -
28A ARG* 3.9 8.1 - - - +
162A PHE* 3.6 26.9 - - + -
185A LEU* 4.3 4.0 - - + -
15B GLU* 2.8 19.3 + - - +
16B GLU* 1.3 72.9 - - - +
18B GLU* 1.3 58.8 + - - +
19B THR 3.1 0.4 - - - -
20B VAL* 5.0 0.4 - - - -
21B ILE* 3.1 50.1 + - + +
158B PRO* 3.6 29.8 - - + -
161B SER* 4.5 0.2 - - - -
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLU* 3.1 25.8 + - + +
17B MET* 1.3 75.8 - - - +
19B THR* 1.3 57.7 + - - +
22B PRO* 3.2 22.0 - - - +
71B VAL* 5.6 1.4 - - - +
73B PRO* 4.0 10.8 - - - +
74B GLY* 2.9 36.7 + - - +
105B ILE* 3.8 18.1 - - + +
106B CYS* 3.2 23.6 - - - +
157B GLY 4.3 0.9 - - - -
158B PRO* 3.2 35.6 - - + +
161B SER* 3.7 20.9 - - - +
164B PHE* 5.3 0.3 - - - -
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Residues in contact with THR 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 4.4 18.5 - - + +
10B LEU* 4.1 24.4 - - + +
14B ALA* 4.1 9.7 - - - +
15B GLU 3.0 14.7 + - - -
16B GLU* 3.6 10.7 - - - -
17B MET 3.1 0.4 - - - -
18B GLU* 1.3 78.8 - - - +
20B VAL* 1.3 64.5 + - + +
21B ILE 3.5 0.2 - - - -
22B PRO* 3.5 4.4 - - - +
23B VAL* 3.1 32.6 + - + +
35B VAL* 5.2 4.5 - - + -
52B ILE* 4.4 13.0 - - + -
73B PRO* 3.5 19.3 - - + +
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Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLU* 3.7 45.1 - - + +
17A MET* 4.0 8.1 - - + +
20A VAL* 4.0 19.5 - - + -
50A VAL* 4.3 15.7 - - + -
16B GLU 2.9 18.4 + - - +
17B MET* 4.5 1.3 - - - +
19B THR* 1.3 75.9 - - + +
21B ILE* 1.3 66.1 + - + +
23B VAL* 3.8 5.1 - - - +
24B ASP* 2.9 22.7 + - - +
52B ILE* 3.9 23.8 - - + -
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Residues in contact with ILE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A MET* 3.9 21.8 - - + -
21A ILE* 3.8 30.7 - - + -
162A PHE* 4.3 8.3 - - + -
17B MET* 3.1 23.6 + - + +
20B VAL* 1.3 74.1 - - + +
22B PRO* 1.3 69.7 - - + +
24B ASP* 3.8 0.3 - - - +
25B VAL* 3.0 32.4 + - + +
161B SER* 3.6 39.7 - - - +
162B PHE* 3.9 33.4 - - + -
165B ALA* 4.6 0.2 - - + -
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Residues in contact with PRO 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL* 5.8 1.3 - - + -
17B MET 3.9 0.2 - - - +
18B GLU* 3.2 31.9 - - - +
19B THR 3.5 5.6 - - - +
21B ILE* 1.3 96.4 - - + +
23B VAL* 1.3 57.4 + - + +
26B MET* 2.9 48.7 + - + +
71B VAL* 4.8 9.0 - - + -
161B SER* 4.6 4.7 - - - +
164B PHE* 4.0 30.5 - - + -
165B ALA* 3.9 17.3 - - + -
168B ILE* 5.2 2.5 - - + -
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A VAL* 3.8 18.2 - - + -
8B VAL* 4.0 24.0 - - + -
19B THR* 3.1 24.4 + - + +
20B VAL* 3.8 4.3 - - - +
22B PRO* 1.3 75.2 - - - +
24B ASP* 1.3 64.5 + - - +
26B MET* 3.9 7.6 - - - +
27B ARG* 3.0 58.5 + - - +
33B VAL* 4.2 6.6 - - + +
35B VAL* 4.0 21.3 - - + -
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Residues in contact with ASP 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLU* 2.5 31.8 - - - +
16A GLU* 3.3 21.0 - - + +
17A MET* 3.3 18.8 - - + +
48A ARG* 3.4 21.4 - - - +
50A VAL* 5.2 0.2 - - - +
20B VAL 2.9 17.8 + - - +
21B ILE 3.8 0.4 - - - +
23B VAL* 1.3 78.8 - - - +
25B VAL* 1.3 62.2 + - - +
27B ARG* 3.1 5.0 + - - +
28B ARG* 2.8 48.7 + - - +
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Residues in contact with VAL 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A MET* 4.2 17.9 - - + -
21B ILE* 3.0 25.6 + - + +
24B ASP* 1.3 74.6 - - - +
26B MET* 1.3 62.0 + - - +
28B ARG* 3.2 12.0 + - - +
29B ALA* 3.2 19.9 + - - +
162B PHE* 4.2 13.7 - - + +
165B ALA* 3.7 26.7 - - + -
166B LEU* 4.0 26.2 - - + -
169B VAL* 4.2 8.7 - - + -
181B VAL* 4.2 7.6 - - + +
185B LEU* 4.4 9.0 - - + -
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Residues in contact with MET 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B ALA* 3.8 25.8 - - + -
8B VAL* 3.8 28.5 - - + -
22B PRO* 2.9 39.8 + - + +
23B VAL* 4.2 0.9 - - - +
25B VAL* 1.3 76.3 - - + +
27B ARG* 1.3 62.7 + - - +
29B ALA* 3.1 10.5 + - - +
31B ILE* 3.1 43.5 + - + +
33B VAL* 3.7 16.6 - - + -
69B VAL* 4.5 0.7 - - - -
71B VAL* 4.1 13.0 - - + -
165B ALA* 5.0 4.0 - - + +
168B ILE* 3.9 28.9 - - + -
169B VAL* 4.4 6.1 - - + -
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Residues in contact with ARG 27 (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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48A ARG* 2.9 40.8 + - + -
49A ASP* 3.7 25.8 + - - +
50A VAL* 3.9 2.4 - - - +
23B VAL* 3.0 39.9 + - - +
24B ASP 3.1 3.6 + - - +
26B MET* 1.3 71.7 - - - +
28B ARG* 1.3 64.8 + - - +
30B GLY* 3.1 13.7 + - - -
31B ILE 3.8 11.2 - - - +
33B VAL* 2.9 43.8 + - + +
35B VAL* 4.3 5.7 - - - +
55B ASP* 3.0 23.6 + - - -
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Residues in contact with ARG 28 (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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15A GLU* 3.0 29.1 + - - +
17A MET* 3.9 3.2 - - - +
48A ARG* 3.5 40.9 - - - +
158A PRO* 4.0 10.5 - - - +
24B ASP* 2.8 33.0 + - - +
25B VAL* 3.2 14.6 + - - +
27B ARG* 1.3 77.3 - - - +
29B ALA* 1.3 57.8 + - - +
30B GLY 3.2 3.1 + - - -
181B VAL* 3.8 23.5 + - + +
184B PRO* 4.8 15.4 + - - +
185B LEU* 3.7 29.2 - - - +
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Residues in contact with ALA 29 (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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25B VAL 3.2 4.8 + - - +
26B MET 3.1 10.5 + - - +
27B ARG 3.1 0.8 - - - -
28B ARG* 1.3 78.3 - - - +
30B GLY* 1.3 56.7 + - - +
31B ILE* 3.3 5.8 - - + -
169B VAL* 3.6 41.7 - - + -
173B ASN* 3.1 19.1 - - - +
177B VAL* 4.3 10.3 - - + +
181B VAL* 3.8 12.6 - - + -
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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
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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