Contacts of the helix formed by residues 21 - 30 (chain R) in PDB entry 1HI0
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 ASN 21 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119P VAL* 3.7 9.7 - - - +
484P PRO* 6.0 2.9 - - - -
19R ALA* 2.8 21.0 + - - +
20R ASN* 1.3 75.4 - - - +
22R ILE* 1.3 64.2 + - - +
23R LYS* 2.8 25.1 + - - +
24R ALA* 2.9 16.9 + - - +
25R GLN* 3.1 22.2 + - - +
155R TYR* 3.1 26.8 + - - +
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Residues in contact with ILE 22 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115P ALA* 4.5 15.3 - - + -
119P VAL* 3.7 28.3 - - + -
484P PRO* 5.5 4.9 - - + -
21R ASN* 1.3 74.4 + - - +
23R LYS* 1.3 56.0 + - + +
25R GLN* 3.2 5.6 + - - +
26R GLN* 2.8 63.3 + - + +
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Residues in contact with LYS 23 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F T 3.4 33.8 - - - +
4F T 4.4 7.0 + - - +
21R ASN* 2.8 12.9 + - - +
22R ILE* 1.3 76.3 - - + +
24R ALA* 1.3 63.5 + - - +
26R GLN* 3.2 12.3 + - - +
27R ALA* 2.9 22.9 + - - +
155R TYR 4.3 0.7 - - - +
156R PHE* 3.5 25.8 + - + +
157R SER* 4.8 2.0 - - - +
158R ASN* 3.2 36.4 + - - +
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Residues in contact with ALA 24 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18R PHE* 3.7 11.7 - - + -
19R ALA 3.2 26.0 - - - +
21R ASN* 2.9 20.4 + - - +
23R LYS* 1.3 71.3 - - - +
25R GLN* 1.3 64.8 + - - +
27R ALA* 3.0 14.6 + - - +
28R SER 3.1 9.4 + - - -
154R PRO 3.4 24.9 - - - +
155R TYR 3.9 1.1 - - - +
156R PHE* 3.7 15.3 - - + +
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Residues in contact with GLN 25 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119P VAL* 3.0 29.5 + - + +
120P SER* 3.5 28.2 - - - +
121P GLU* 4.2 4.4 - - - +
15R GLN* 4.5 13.7 + - - +
18R PHE* 3.5 18.0 - - - +
19R ALA 3.3 17.0 - - - +
21R ASN 3.1 18.8 + - - +
22R ILE* 3.6 4.5 - - - +
24R ALA* 1.3 74.8 - - - +
26R GLN* 1.3 63.1 + - + +
28R SER* 2.6 27.9 + - - -
29R LYS* 3.1 33.5 + - - +
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Residues in contact with GLN 26 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F T 5.1 6.1 + - - -
4F T 4.9 1.8 - - - +
22R ILE* 2.8 44.3 + - + +
23R LYS* 3.7 15.0 - - - +
25R GLN* 1.3 73.8 - - + +
27R ALA* 1.3 53.7 + - - +
29R LYS* 3.9 6.2 - - + +
30R ARG* 2.6 66.4 + - - +
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Residues in contact with ALA 27 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F T 3.6 18.6 + - - +
23R LYS 2.9 11.7 + - - +
24R ALA 3.3 9.6 - - - +
26R GLN* 1.3 79.3 - - - +
28R SER* 1.3 61.9 + - - +
29R LYS 3.4 0.2 + - - -
30R ARG* 3.6 9.3 + - - +
156R PHE* 3.7 31.0 - - + -
200R TYR* 2.7 34.4 + - + +
366R TYR* 4.6 1.4 - - - -
368R GLY* 5.6 1.6 - - - -
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Residues in contact with SER 28 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9R LEU* 3.3 14.1 - - - +
15R GLN* 5.4 0.2 + - - -
18R PHE* 3.4 49.1 - - - -
24R ALA 3.1 5.0 + - - -
25R GLN* 2.6 29.3 + - - -
27R ALA* 1.3 79.0 - - - +
29R LYS* 1.3 64.1 + - - +
30R ARG 4.7 0.3 - - - +
366R TYR* 2.7 22.9 + - - -
368R GLY* 5.6 0.5 - - - -
376R HIS* 3.1 12.1 - - - -
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Residues in contact with LYS 29 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118P PRO 5.5 1.0 + - - -
119P VAL 3.5 23.8 + - - -
120P SER* 5.0 1.4 - - - +
121P GLU* 5.3 3.6 - - - +
9R LEU* 4.3 9.9 - - + -
25R GLN* 3.1 35.6 + - - +
26R GLN* 3.9 5.2 - - + +
28R SER* 1.3 84.5 + - - +
30R ARG* 1.3 67.3 + - - +
31R SER* 3.1 5.2 + - - -
376R HIS* 2.9 16.8 + - - -
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Residues in contact with ARG 30 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3F T 4.0 24.1 + - - -
4F T 3.7 37.0 + - + -
26R GLN* 2.6 54.7 + - - +
27R ALA* 3.7 12.6 - - - +
28R SER 3.5 1.5 - - - +
29R LYS* 1.3 67.6 - - - +
31R SER* 1.3 70.3 + - - +
33R LYS* 4.0 28.1 - - + +
200R TYR* 4.4 4.9 - - - +
368R GLY* 4.5 4.9 - - - +
369R ALA* 3.9 6.4 - - - +
376R HIS* 3.0 17.2 + - - -
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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