Contacts of the helix formed by residues 120 - 135 (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 SER 120 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118R PRO* 4.2 3.1 - - - +
119R VAL* 1.3 84.2 - - - +
121R GLU* 1.3 65.2 + - - +
122R ARG* 3.1 15.7 + - - +
123R ASP* 3.1 29.3 + - - +
124R ASN* 3.1 18.6 + - - +
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Residues in contact with GLU 121 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120R SER* 1.3 73.6 - - - +
122R ARG* 1.3 63.5 + - - +
124R ASN* 3.2 28.4 + - - +
125R LEU* 2.9 43.0 + - + +
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Residues in contact with ARG 122 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120R SER* 3.1 12.3 + - - +
121R GLU* 1.3 78.2 - - - +
123R ASP* 1.3 85.4 + - - +
125R LEU* 2.9 14.8 + - - +
126R LEU* 2.8 32.1 + - + +
412R VAL* 3.7 6.4 - - - +
415R LEU* 3.5 31.5 - - - +
416R ASP* 2.6 36.5 + - - +
423R ASN* 2.5 47.5 + - - +
426R ILE* 4.1 24.5 - - + +
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Residues in contact with ASP 123 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118R PRO* 4.3 2.2 - - + -
119R VAL* 4.2 5.5 - - - +
120R SER* 3.1 18.8 + - - +
122R ARG* 1.3 105.0 + - - +
124R ASN* 1.3 64.5 + - - +
126R LEU* 3.2 8.3 + - - +
127R PHE* 3.0 33.7 + - + -
412R VAL* 3.5 21.9 - - + +
416R ASP* 5.2 0.3 - - - +
484R PRO* 5.0 1.0 - - - +
485R TYR* 2.5 41.3 + - + +
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Residues in contact with ASN 124 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118R PRO* 3.7 24.0 - - + +
120R SER 3.1 9.3 + - - +
121R GLU* 3.2 36.6 + - - +
123R ASP* 1.3 76.8 - - - +
125R LEU* 1.3 65.5 + - - +
127R PHE* 3.5 2.4 + - - +
128R ARG* 2.8 57.3 + - - +
339R LEU* 3.9 9.4 - - - +
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Residues in contact with LEU 125 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121R GLU* 2.9 39.3 + - + +
122R ARG* 2.9 10.4 + - - +
124R ASN* 1.3 79.4 - - - +
126R LEU* 1.3 51.8 + - - +
128R ARG* 3.2 4.4 + - - +
129R ALA* 2.6 37.4 + - - +
426R ILE* 4.4 13.5 - - + +
427R LYS 3.9 7.4 - - - +
428R ASP* 3.8 28.0 - - - +
429R MET* 3.5 40.1 - - + +
432R ALA* 4.2 10.1 - - + -
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Residues in contact with LEU 126 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122R ARG* 2.8 36.8 + - + +
123R ASP 3.6 6.3 - - - +
125R LEU* 1.3 74.1 - - - +
127R PHE* 1.3 52.7 + - - +
129R ALA* 3.0 5.8 + - - +
130R ALA* 2.7 34.3 + - - +
408R ILE* 3.8 18.9 - - + +
411R LEU* 3.9 21.8 - - + -
412R VAL* 4.1 17.7 - - + -
415R LEU* 3.9 20.9 - - + -
426R ILE* 4.2 24.7 - - + -
432R ALA* 5.0 4.7 - - + +
435R PHE* 4.4 7.6 - - + -
436R LEU* 4.8 13.0 - - + -
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Residues in contact with PHE 127 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118R PRO* 4.3 13.2 - - + -
123R ASP* 3.0 31.2 + - + +
124R ASN 3.9 3.1 - - - +
126R LEU* 1.3 75.0 - - - +
128R ARG* 1.3 57.4 + - - +
130R ALA* 3.1 6.1 + - - +
131R VAL* 3.0 29.1 + - - +
335R TRP* 3.7 26.9 - + - -
336R LEU* 4.0 19.5 - - + -
339R LEU* 3.9 17.0 - - + -
404R LEU* 4.4 7.9 - - + +
405R LEU* 4.0 22.0 - - + -
408R ILE* 3.5 37.7 - - + -
409R THR* 4.5 3.4 - - - -
485R TYR* 4.1 34.1 - + - -
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Residues in contact with ARG 128 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124R ASN* 2.8 46.6 + - - +
125R LEU* 3.6 6.1 - - - +
127R PHE* 1.3 77.0 - - - +
129R ALA* 1.3 64.5 - - - +
131R VAL* 3.4 1.2 + - - +
132R ARG* 3.1 27.0 + - - +
339R LEU* 3.5 32.3 - - + +
342R ASP* 2.9 34.9 + - - +
343R GLU* 2.6 52.2 + - - +
346R ASN* 3.7 3.8 - - - +
429R MET* 3.8 12.8 - - + -
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Residues in contact with ALA 129 (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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125R LEU 2.6 20.6 + - - +
126R LEU* 3.3 10.1 - - + +
128R ARG* 1.3 69.8 - - - +
130R ALA* 1.3 67.6 + - - +
132R ARG* 2.9 3.5 + - - +
133R LEU* 2.8 26.7 + - - +
429R MET* 3.9 8.7 - - + +
432R ALA* 4.1 7.0 - - + -
433R CYS* 4.0 31.6 - - - +
436R LEU* 3.7 14.4 - - + -
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Residues in contact with ALA 130 (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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126R LEU 2.7 12.0 + - - +
127R PHE 3.2 9.9 - - - +
129R ALA* 1.3 77.0 - - - +
131R VAL* 1.3 61.7 + - - +
133R LEU 3.5 0.2 + - - -
134R MET* 3.0 29.5 + - - +
404R LEU* 3.5 20.9 - - + -
408R ILE* 3.7 25.6 - - + -
436R LEU* 3.3 10.3 - - - +
440R TRP* 3.8 11.7 - - + -
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Residues in contact with VAL 131 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127R PHE 3.0 18.6 + - - +
128R ARG* 3.6 8.7 - - - +
129R ALA 3.1 0.2 - - - -
130R ALA* 1.3 76.7 - - - +
132R ARG* 1.3 62.5 + - - +
135R PHE* 2.9 32.2 + - + +
339R LEU* 4.7 1.1 - - + -
340R ILE* 3.8 38.1 - - + +
343R GLU* 3.9 16.4 - - + -
344R LEU* 3.9 25.1 - - + -
347R MET* 3.8 16.6 - - - +
404R LEU* 4.2 11.0 - - + -
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Residues in contact with ARG 132 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128R ARG 3.1 12.6 + - - +
129R ALA 2.9 7.1 + - - +
131R VAL* 1.3 76.8 - - - +
133R LEU* 1.3 60.5 + - + +
136R SER* 2.8 30.5 + - - -
343R GLU* 2.2 36.1 + - + +
346R ASN* 4.0 8.5 + - - +
347R MET* 3.3 55.4 - - + +
429R MET* 3.2 29.3 - - - +
433R CYS* 4.2 15.3 - - - -
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Residues in contact with LEU 133 (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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129R ALA 2.8 19.9 + - - +
132R ARG* 1.3 74.5 - - + +
134R MET* 1.3 56.6 + - - +
136R SER* 3.1 14.7 + - - +
293R LYS* 3.1 20.1 - - - +
297R LYS* 5.5 2.2 - - - +
298R TYR* 3.4 24.1 - - + +
433R CYS* 3.9 23.6 - - + +
436R LEU* 3.7 21.5 - - + -
437R ASP* 3.4 39.5 - - + +
440R TRP* 3.7 20.6 - - + -
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Residues in contact with MET 134 (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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130R ALA 3.0 17.7 + - - +
131R VAL 3.3 0.2 + - - -
133R LEU* 1.3 78.8 - - - +
135R PHE* 1.3 76.0 + - + +
136R SER 3.5 2.3 + - - -
138R LEU* 3.6 16.3 - - - +
290R VAL* 3.7 18.8 - - + +
293R LYS* 4.1 4.7 - - - +
294R ILE* 3.9 42.4 - - + -
302R PHE* 4.5 3.8 - - + -
400R LEU* 4.8 9.4 - - + +
403R THR* 4.2 21.1 - - + -
404R LEU* 3.2 37.7 - - + +
440R TRP* 3.9 20.0 - - + -
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Residues in contact with PHE 135 (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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131R VAL* 2.9 32.6 + - + +
134R MET* 1.3 94.9 - - + +
136R SER* 1.3 61.3 + - - +
138R LEU* 3.9 6.9 - - - +
286R VAL* 4.5 10.3 - - + -
287R ALA* 6.2 0.7 - - - -
290R VAL* 3.8 26.5 - - + -
340R ILE* 5.1 5.6 - - + -
344R LEU* 3.6 38.1 - - + -
347R MET* 3.6 7.4 - - + +
349R TYR* 2.6 46.2 + + + +
353R TRP* 4.7 7.2 - + - -
357R PHE* 5.2 6.5 - + - -
397R ALA* 6.4 0.7 - - + -
400R LEU* 5.3 5.4 - - + -
401R MET* 4.6 21.8 - - + -
404R LEU* 5.1 2.9 - - + -
663R PRO* 5.3 0.2 - - - +
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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