Contacts of the helix formed by residues 2 - 13 (chain B) in PDB entry 5EJK
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 LEU 2 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B PRO* 1.3 89.1 - - + +
3B ARG* 1.3 61.8 + - + +
5B ALA* 3.5 2.4 + - - +
6B LYS* 3.0 46.8 + - - +
25B ILE* 3.7 21.5 - - + -
29B GLN* 3.7 35.9 - - + +
33B VAL* 5.8 7.0 - - + +
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Residues in contact with ARG 3 (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 PRO* 3.4 1.8 - - - +
2B LEU* 1.3 76.2 - - + +
4B GLU* 1.3 67.4 + - + +
6B LYS* 3.2 12.9 + - + +
7B ASP* 2.9 32.8 + - - +
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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 PRO* 3.6 25.9 + - + +
2B LEU 3.4 0.4 - - - -
3B ARG* 1.3 77.6 - - + +
5B ALA* 1.3 56.5 + - - +
7B ASP* 3.3 8.4 + - - +
8B LEU* 2.9 38.6 + - + +
23B SER* 4.9 9.2 - - - -
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Residues in contact with ALA 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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1B PRO 2.9 19.2 + - - +
2B LEU 3.8 2.0 - - - +
4B GLU* 1.3 72.7 - - - +
6B LYS* 1.3 68.0 + - + +
8B LEU* 3.2 13.1 + - - +
9B HIS* 2.9 24.3 + - - +
19B LEU* 3.9 19.5 - - + +
23B SER* 3.4 19.2 - - - +
25B ILE* 3.5 12.3 - - + -
30B ALA* 6.4 0.7 - - + -
33B VAL* 5.4 5.8 - - + -
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Residues in contact with LYS 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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2B LEU* 3.0 40.1 + - - +
3B ARG* 3.2 12.3 + - + +
5B ALA* 1.3 76.6 - - - +
7B ASP* 1.3 59.7 + - - +
9B HIS* 3.3 3.2 + - - +
10B THR* 2.9 37.5 + - + +
33B VAL* 4.3 35.2 - - + -
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Residues in contact with ASP 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 ARG* 2.9 24.7 + - - +
4B GLU* 3.6 7.3 - - - +
6B LYS* 1.3 79.1 - - - +
8B LEU* 1.3 63.9 + - + +
10B THR* 2.2 31.1 + - - +
11B ALA* 3.0 10.2 + - - +
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Residues in contact with LEU 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* 2.9 24.1 + - + +
5B ALA* 3.2 11.9 + - + +
7B ASP* 1.3 76.7 - - + +
9B HIS* 1.3 56.8 + - - +
11B ALA* 3.4 3.3 + - - +
12B LEU* 2.9 36.9 + - + +
13B HIS 3.7 1.2 + - - -
14B ILE* 4.4 12.6 - - + +
19B LEU* 3.6 21.3 - - + -
22B ALA* 4.8 17.5 - - + -
23B SER* 5.2 6.1 - - - -
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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
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5B ALA 2.9 11.7 + - - +
6B LYS* 3.8 5.6 - - - +
8B LEU* 1.3 73.8 - - - +
10B THR* 1.3 66.8 + - + +
13B HIS* 2.6 45.8 + - - +
14B ILE 2.8 30.0 + - - +
15B GLY* 5.3 0.4 - - - -
19B LEU* 3.7 18.3 - - + +
33B VAL* 4.8 12.1 - - + -
34B VAL* 4.1 15.0 - - + -
37B CYS* 3.3 28.0 - - + +
40B CYS* 2.7 39.2 - - - +
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Residues in contact with THR 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 LYS* 2.9 28.3 + - + +
7B ASP* 2.2 37.5 + - - +
9B HIS* 1.3 78.3 - - + +
11B ALA* 1.3 60.4 + - - +
13B HIS* 3.2 24.3 + - - -
37B CYS* 6.2 0.4 - - - -
173B GLY* 5.0 8.1 - - - +
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Residues in contact with ALA 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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137A ARG* 6.3 0.4 - - - +
7B ASP 3.0 9.9 + - - +
8B LEU* 4.1 2.9 - - - +
10B THR* 1.3 85.3 + - - +
12B LEU* 1.3 70.4 + - + +
13B HIS* 3.9 0.5 - - - -
170B LEU* 3.3 17.8 - - - +
173B GLY* 6.0 0.3 - - - -
174B ASP* 4.6 8.9 - - - +
191B LYS* 4.5 12.6 + - - +
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Residues in contact with LEU 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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138A TRP* 4.8 8.3 - - + -
8B LEU* 2.9 16.5 + - + +
11B ALA* 1.3 79.5 - - + +
13B HIS* 1.3 71.4 + - - +
14B ILE* 3.4 21.9 + - + -
166B LYS* 3.5 6.1 + - - -
170B LEU* 3.5 13.2 - - + +
191B LYS* 3.9 43.7 - - + +
194B TYR* 4.1 16.6 - - + -
195B ALA* 4.2 13.4 - - + +
199B PHE* 3.7 27.6 - - + -
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Residues in contact with HIS 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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9B HIS* 2.6 56.2 + - + -
10B THR* 3.2 20.4 + - - -
11B ALA 3.9 0.7 - - - -
12B LEU* 1.3 71.0 - - - +
14B ILE* 1.3 67.1 + - - +
15B GLY* 3.7 1.7 + - - -
37B CYS* 3.9 17.9 - - - -
39B HIS* 4.2 13.0 - - + -
40B CYS* 3.7 9.3 - - - -
166B LYS* 2.7 32.5 + - - +
169B VAL* 3.3 39.2 + - + +
170B LEU* 3.7 16.6 - - + -
173B GLY* 4.5 7.7 - - - -
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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
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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