Contacts of the helix formed by residues 3 - 15 (chain B) in PDB entry 2EHO
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 CYS 3 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MSE 3.6 3.4 - - - +
2B PHE* 1.3 82.1 - - - +
4B GLU* 1.3 63.2 + - - +
5B LYS 3.3 3.6 - - - +
6B ALA* 3.4 5.5 + - + +
7B MSE 3.3 23.0 + - + +
35B GLU* 4.7 3.6 + - - -
68B SER* 3.5 10.8 - - - -
71B ARG* 3.4 44.8 - - + +
72B ASN* 3.3 42.5 - - - +
29D HIS* 5.7 0.2 - - - +
71D TRP* 3.8 12.6 - - + -
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Residues in contact with GLU 4 (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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1B MSE 5.7 0.2 - - - +
2B PHE* 2.9 20.5 - - + +
3B CYS* 1.3 75.7 - - - +
5B LYS* 1.3 65.6 + - - +
7B MSE 3.1 20.4 + - - +
8B GLU* 3.3 8.1 + - - +
11B ARG* 3.8 21.6 + - - +
35B GLU* 5.5 0.4 + - - -
29D HIS* 3.5 29.8 + - - -
31D LYS* 4.1 9.2 + - - -
46D PHE* 5.9 2.5 - - + -
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Residues in contact with LYS 5 (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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3B CYS* 3.3 0.8 - - - -
4B GLU* 1.3 78.5 - - - +
6B ALA* 1.3 63.4 + - - +
7B MSE 3.3 0.3 + - - -
8B GLU* 3.3 22.2 + - + +
9B LEU* 3.7 8.7 + - - +
25B ASN* 5.2 3.4 + - - -
28B GLY* 4.4 15.6 - - - +
31B GLN* 3.0 52.6 - - + +
32B VAL* 4.3 10.2 - - + +
35B GLU* 3.6 27.5 + - - +
72B ASN* 5.8 0.4 - - - +
15F ARG* 4.1 25.2 - - - +
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Residues in contact with ALA 6 (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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3B CYS* 3.4 11.9 + - + +
4B GLU 3.2 0.4 - - - -
5B LYS* 1.3 78.8 - - - +
7B MSE 1.3 56.9 + - - +
9B LEU* 2.9 28.7 + - + +
10B ILE* 3.4 10.9 + - - +
32B VAL* 4.0 21.9 - - + +
72B ASN* 3.7 22.1 + - - +
75B CYS* 3.8 25.6 - - + +
76B THR 5.2 0.7 - - - +
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Residues in contact with MSE 7 (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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3B CYS 3.3 15.3 - - - +
4B GLU* 3.1 11.4 + - - +
6B ALA* 1.3 73.4 - - - +
8B GLU* 1.3 58.6 + - - +
9B LEU 2.8 10.2 + - - -
10B ILE* 2.7 26.0 - - + +
11B ARG* 3.0 39.0 + - - +
71B ARG* 4.3 8.5 - - - +
75B CYS* 4.6 2.0 - - - -
25D ILE* 3.3 33.7 - - + -
26D LEU* 3.9 16.4 - - + +
29D HIS* 3.4 54.7 - - + +
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Residues in contact with GLU 8 (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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4B GLU 3.3 7.3 + - - +
5B LYS* 3.3 21.3 + - + +
7B MSE 1.3 77.6 - - - +
9B LEU* 1.3 58.3 + - - +
11B ARG* 3.2 33.5 + - - +
12B GLU* 3.4 21.7 + - - +
15B ARG* 4.0 7.8 + - - -
25B ASN* 5.3 1.6 - - - +
12F GLU* 4.5 14.7 - - - +
15F ARG* 3.3 51.3 - - + +
16F ALA* 6.3 0.2 - - - -
17F PRO* 5.9 0.7 - - - +
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Residues in contact with LEU 9 (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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5B LYS 3.7 4.2 + - - +
6B ALA* 2.9 17.6 + - - +
7B MSE 2.8 1.6 + - - -
8B GLU* 1.3 79.4 - - - +
10B ILE* 1.3 62.8 + - + +
11B ARG 3.0 1.9 + - - -
12B GLU* 3.4 13.5 + - - +
13B LEU 3.7 2.6 + - - -
25B ASN* 3.0 45.3 - - + +
28B GLY* 4.4 6.3 - - - -
29B LEU* 4.3 17.5 - - + +
32B VAL* 4.1 24.0 - - + -
75B CYS 5.7 0.4 - - - +
76B THR* 5.1 7.2 - - - +
79B TYR* 3.2 57.8 - - + -
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Residues in contact with ILE 10 (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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6B ALA 3.6 11.7 - - - +
7B MSE 2.7 36.4 + - - +
9B LEU* 1.3 76.5 - - + +
11B ARG* 1.3 66.7 + - + +
13B LEU* 3.3 10.0 + - - +
14B HIS* 3.0 23.3 + - + +
75B CYS* 4.1 27.8 - - + +
78B ALA* 5.8 0.7 - - + -
79B TYR* 4.6 5.8 - - + -
22D LEU* 4.2 25.6 - - + +
25D ILE* 3.4 35.0 - - + -
26D LEU* 3.5 28.5 - - + -
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Residues in contact with ARG 11 (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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4B GLU* 3.8 16.0 + - - +
7B MSE 3.0 52.1 + - - +
8B GLU* 3.2 30.6 + - - +
10B ILE* 1.3 82.8 - - + +
12B GLU* 1.3 54.6 + - - +
13B LEU 2.7 16.1 + - - -
14B HIS* 2.8 18.6 + - + +
15B ARG* 2.9 51.7 + - - +
26D LEU* 4.3 10.5 - - + +
29D HIS* 4.6 6.3 + - - -
30D GLU* 5.9 1.0 + - - -
12F GLU* 6.1 1.6 - - - -
20F GLN* 4.5 0.2 - - - -
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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
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8B GLU 3.4 13.5 + - - +
9B LEU* 3.4 9.8 + - + +
11B ARG* 1.3 77.5 - - - +
13B LEU* 1.3 62.8 + - - +
15B ARG* 5.6 0.2 - - - +
16B ALA* 4.1 0.7 - - - +
22B PRO* 3.6 19.3 - - + +
23B ALA 3.5 20.3 + - - +
25B ASN* 3.8 19.7 - - - +
79B TYR* 3.5 28.2 + - - -
83B ARG* 4.1 0.2 + - - -
17F PRO* 3.5 34.8 - - + +
20F GLN* 3.0 32.2 + - - -
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Residues in contact with LEU 13 (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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10B ILE* 3.3 11.4 + - - +
11B ARG 2.7 1.2 + - - -
12B GLU* 1.3 90.5 - - - +
14B HIS* 1.3 60.9 + - - +
15B ARG 3.2 1.8 - - - -
16B ALA* 3.3 12.3 + - - +
21B LEU* 6.1 0.2 - - + -
22B PRO* 3.7 28.3 - - + -
79B TYR* 3.7 48.0 - - + +
82B ASP* 3.8 19.3 - - + -
83B ARG* 4.0 14.6 - - + +
86B ARG* 3.0 36.7 + - - +
22D LEU* 4.1 12.8 - - + -
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Residues in contact with HIS 14 (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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10B ILE* 3.0 15.1 + - + +
11B ARG* 2.8 10.8 + - + +
13B LEU* 1.3 74.6 - - - +
15B ARG* 1.3 64.3 + - + +
16B ALA 3.1 7.9 + - - +
17B PRO* 5.8 0.2 - - - +
1016B SO4 2.3 55.4 + - - -
22D LEU* 4.9 8.3 - - + +
23D ASP* 5.7 7.0 + - - -
26D LEU* 3.9 21.7 - - + +
170D GLU* 5.0 2.0 - - - -
101F ALA* 6.1 0.9 - - - +
105F HIS* 3.0 19.7 + + - -
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Residues in contact with ARG 15 (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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8B GLU* 4.0 8.3 + - - -
11B ARG* 2.9 53.9 + - - +
14B HIS* 1.3 81.7 - - + +
16B ALA* 1.3 56.7 + - - +
17B PRO* 3.1 12.1 - - - +
1016B SO4 4.1 14.6 + - - -
12F GLU* 4.5 13.3 + - - +
16F ALA* 4.9 6.8 - - - +
20F GLN* 2.9 45.9 + - + +
21F LEU 4.0 8.9 + - - +
22F PRO* 3.3 53.1 - - + +
23F ALA* 3.6 8.3 - - - +
105F HIS* 4.3 8.9 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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