Contacts of the helix formed by residues 13 - 17 (chain W) in PDB entry 5L4K
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 SER 13 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11W ASP* 3.9 7.0 + - - -
12W ASN* 1.3 77.2 - - - +
14W GLU* 1.3 59.8 + - - +
15W TYR 3.5 4.1 + - - -
16W MET* 2.9 27.4 + - - +
80W PRO* 3.1 16.4 - - - +
81W LYS 3.3 18.1 + - - +
82W GLY 3.5 8.3 - - - -
83W LYS* 5.6 0.2 - - - -
84W ILE* 4.0 5.6 - - - -
114W GLY 3.0 19.8 + - - -
115W SER* 3.9 20.0 - - - -
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Residues in contact with GLU 14 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35O HIS* 3.4 44.6 + - + +
38O THR* 5.3 6.6 - - - +
39O LEU* 4.0 11.8 - - - +
72O ASN* 3.4 29.4 - - - +
13W SER* 1.3 73.4 - - - +
15W TYR* 1.3 61.3 + - - +
16W MET 3.2 0.9 + - - -
17W ARG* 3.2 33.0 + - - +
80W PRO* 4.5 0.9 - - - -
81W LYS* 4.0 9.7 - - - +
82W GLY 4.0 17.0 + - - +
83W LYS* 5.9 2.8 - - - +
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Residues in contact with TYR 15 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33O LEU* 4.1 15.1 - - + +
35O HIS* 3.5 29.6 - + + -
36O GLN* 3.9 20.4 - - + -
13W SER* 3.0 3.0 - - - +
14W GLU* 1.3 74.7 - - - +
16W MET* 1.3 54.6 + - - +
17W ARG 2.9 11.4 + - - -
18W ASN* 3.1 34.1 + - - +
20W ASP* 4.6 6.5 + - - -
21W PHE* 5.1 0.4 - + - -
25W ARG* 3.8 20.3 - - - -
114W GLY 3.2 28.9 - - - +
115W SER* 3.9 11.4 - - - +
116W PRO* 4.9 1.8 - - + -
143W PHE 4.4 0.4 - - - -
144W GLY* 3.8 25.5 - - - -
145W GLU 3.9 9.7 + - - -
148W VAL* 4.2 17.8 - - + +
175W PRO* 6.1 0.7 - - - +
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Residues in contact with MET 16 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10W VAL* 4.9 2.2 - - - -
11W ASP* 3.2 26.0 - - - +
12W ASN* 3.7 15.3 - - - +
13W SER* 2.9 21.8 + - - +
14W GLU 3.9 0.7 - - - -
15W TYR* 1.3 72.4 - - - +
17W ARG* 1.3 58.8 + - - +
18W ASN 3.8 1.3 - - - -
25W ARG* 3.3 27.4 - - - +
26W LEU* 3.5 63.3 - - + +
29W GLN* 4.2 18.4 - - - -
78W VAL* 4.2 6.5 - - + -
79W GLN 4.2 1.1 - - - -
80W PRO* 3.6 24.3 - - + +
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Residues in contact with ARG 17 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34O TRP* 2.8 32.7 - - + +
35O HIS* 5.5 3.4 - - - +
38O THR* 4.7 5.5 + - - -
69O HIS 4.2 10.8 - - - +
70O ARG 3.3 25.0 + - - -
71O VAL* 3.5 12.8 - - - +
72O ASN* 2.9 42.5 + - - +
14W GLU* 3.2 17.5 + - - +
15W TYR 2.9 2.6 + - - -
16W MET* 1.3 80.2 - - - +
18W ASN* 1.3 66.0 + - - +
24W THR* 4.0 21.1 - - + -
26W LEU* 5.9 1.8 - - + -
80W PRO* 3.4 36.0 + - + +
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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
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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