Contacts of the helix formed by residues 318 - 322 (chain A) in PDB entry 1HT0
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 ILE 318 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A PHE* 3.8 7.4 - - + -
94A THR* 3.4 26.7 - - + +
109A ASN* 2.8 29.3 + - - +
110A TYR* 3.3 42.0 - - + +
116A LEU* 3.6 21.1 - - + -
317A ALA* 1.3 72.9 - - - +
319A PHE* 1.3 67.6 + - - +
320A GLY 3.2 1.6 - - - -
321A GLY 3.1 4.2 + - - -
1377A NAD 3.4 9.6 - - - +
306B MET* 5.7 2.5 - - + -
309B LEU* 3.4 29.6 + - + +
310B THR* 4.2 12.4 - - + +
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Residues in contact with PHE 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU* 5.5 2.5 - - + -
93A PHE* 3.7 26.0 - + + -
94A THR* 4.0 12.8 - - - +
109A ASN* 4.0 3.8 - - - +
172A ILE 3.5 20.4 - - - -
173A GLY* 3.6 18.6 - - - -
174A CYS* 4.0 1.3 - - - -
177A SER* 3.5 21.3 - - - -
178A THR* 3.4 20.0 - - - -
317A ALA 4.2 0.2 - - - -
318A ILE* 1.3 74.5 - - - +
320A GLY* 1.3 62.6 + - - +
321A GLY 3.1 0.2 - - - -
322A PHE* 3.0 42.4 + - + +
324A SER* 3.9 28.7 - - - -
328A VAL* 3.8 18.2 - - + -
331A LEU* 5.5 0.7 - - + -
1377A NAD 3.0 14.1 + - - -
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Residues in contact with GLY 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A SER 3.8 4.3 - - - -
178A THR* 3.5 29.1 + - - +
181A GLY* 3.4 21.8 - - - +
182A SER* 3.6 13.6 + - - -
185A LYS* 3.6 8.3 - - - +
186A VAL* 3.6 10.1 - - - +
317A ALA* 4.9 1.9 - - - -
318A ILE 3.2 2.2 + - - +
319A PHE* 1.3 76.4 - - - +
321A GLY* 1.3 56.4 + - - +
322A PHE* 3.1 6.5 + - - -
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Residues in contact with GLY 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLU 5.2 3.9 - - - +
108A SER 4.9 2.3 - - - -
109A ASN* 3.4 30.0 + - - +
185A LYS* 3.3 18.2 - - - +
186A VAL* 3.8 11.3 - - - +
317A ALA* 4.2 4.9 - - - +
318A ILE 3.1 6.0 + - - -
319A PHE 3.0 2.2 + - - -
320A GLY* 1.3 75.5 - - - +
322A PHE* 1.3 62.3 + - - +
323A LYS* 3.5 3.1 + - - +
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Residues in contact with PHE 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A THR* 5.2 0.3 - - - +
109A ASN* 3.0 16.9 + - - +
177A SER* 3.4 31.2 - - - -
180A TYR* 4.8 11.0 - + - -
181A GLY* 3.5 19.5 - - - -
184A VAL* 6.2 2.0 - - + -
185A LYS* 3.5 24.9 - - + -
319A PHE* 3.0 30.0 + - + +
320A GLY 3.1 5.3 + - - -
321A GLY* 1.3 77.4 - - - +
323A LYS* 1.3 59.8 + - - +
324A SER* 2.9 8.7 + - - -
327A SER* 3.4 29.6 - - - +
331A LEU* 4.0 35.4 - - + -
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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