Contacts of the helix formed by residues 120 - 135 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118P PRO* 4.2 2.6 - - - +
119P VAL* 1.3 78.9 - - - +
121P GLU* 1.3 65.2 + - - +
122P ARG* 3.4 10.0 + - - +
123P ASP* 3.1 22.0 + - - +
124P ASN* 3.1 18.9 + - - +
15R GLN* 5.1 2.9 - - - -
20R ASN* 3.0 27.1 + - - -
25R GLN* 3.5 23.1 - - - +
29R LYS* 5.3 1.6 - - - -
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Residues in contact with GLU 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120P SER* 1.3 74.8 - - - +
122P ARG* 1.3 63.9 + - - +
124P ASN* 3.2 27.8 + - - +
125P LEU* 2.9 44.7 + - + +
15R GLN* 3.9 22.9 - - + +
25R GLN* 4.2 6.4 - - - +
29R LYS* 5.3 3.7 - - - +
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Residues in contact with ARG 122 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120P SER* 3.5 6.5 - - - +
121P GLU* 1.3 77.2 - - - +
123P ASP* 1.3 72.7 + - - +
125P LEU* 2.9 14.9 + - - +
126P LEU* 2.8 30.3 + - + +
412P VAL* 3.7 4.0 - - - +
415P LEU* 3.5 31.1 - - - +
416P ASP* 2.6 19.2 + - - +
423P ASN* 2.5 47.5 + - - +
426P ILE* 4.1 24.5 - - + +
15R GLN* 4.8 5.2 - - - +
20R ASN* 2.5 45.2 - - - +
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Residues in contact with ASP 123 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118P PRO* 4.3 2.5 - - + -
119P VAL* 4.2 0.2 - - - +
120P SER* 3.1 16.2 + - - +
122P ARG* 1.3 104.4 + - - +
124P ASN* 1.3 65.5 + - - +
126P LEU* 3.2 8.8 + - - +
127P PHE* 3.0 33.7 + - + -
412P VAL* 3.5 13.9 - - + +
485P TYR* 2.5 38.7 + - + +
20R ASN* 3.0 22.8 + - - +
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Residues in contact with ASN 124 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118P PRO* 3.7 24.1 - - + +
120P SER 3.1 10.4 + - - +
121P GLU* 3.2 36.2 + - - +
122P ARG 3.1 0.2 - - - -
123P ASP* 1.3 76.0 - - - +
125P LEU* 1.3 65.7 + - - +
127P PHE* 3.5 2.6 + - - +
128P ARG* 2.8 57.5 + - - +
339P LEU* 3.9 9.4 - - - +
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Residues in contact with LEU 125 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121P GLU* 2.9 40.6 + - + +
122P ARG* 2.9 11.1 + - - +
124P ASN* 1.3 78.8 - - - +
126P LEU* 1.3 52.0 + - - +
128P ARG* 3.2 5.1 + - - +
129P ALA* 2.6 37.6 + - - +
426P ILE* 4.4 13.9 - - + +
427P LYS 3.9 7.0 - - - +
428P ASP* 3.8 28.0 - - - +
429P MET* 3.5 40.1 - - + +
432P ALA* 4.2 10.1 - - + -
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Residues in contact with LEU 126 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122P ARG* 2.8 37.6 + - + +
123P ASP 3.6 5.8 - - - +
125P LEU* 1.3 73.1 - - - +
127P PHE* 1.3 51.5 + - - +
129P ALA* 3.0 5.1 + - - +
130P ALA* 2.7 34.7 + - - +
408P ILE* 3.8 17.6 - - + +
411P LEU* 3.9 21.3 - - + -
412P VAL* 4.1 18.4 - - + -
415P LEU* 3.9 20.9 - - + -
426P ILE* 4.2 24.2 - - + -
432P ALA* 5.0 4.0 - - + -
435P PHE* 4.4 8.5 - - + -
436P LEU* 3.9 13.5 - - + +
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Residues in contact with PHE 127 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118P PRO* 4.3 13.2 - - + -
123P ASP* 3.0 31.2 + - + +
124P ASN 3.9 2.7 - - - +
126P LEU* 1.3 74.8 - - - +
128P ARG* 1.3 60.3 + - - +
130P ALA* 3.1 5.8 + - - +
131P VAL* 3.0 28.8 + - - +
335P TRP* 3.7 26.9 - + - -
336P LEU* 4.0 17.7 - - + -
339P LEU* 3.9 16.6 - - + -
404P LEU* 4.4 7.7 - - + +
405P LEU* 4.0 22.9 - - + -
408P ILE* 3.5 37.2 - - + -
409P THR* 4.5 3.8 - - - -
485P TYR* 4.1 34.3 - + - -
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Residues in contact with ARG 128 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124P ASN* 2.8 47.1 + - - +
125P LEU* 3.6 5.8 - - - +
127P PHE* 1.3 76.9 - - - +
129P ALA* 1.3 64.2 + - - +
131P VAL* 3.4 1.8 + - - +
132P ARG* 3.1 26.9 + - - +
339P LEU* 3.5 32.6 - - + +
342P ASP* 2.9 34.1 + - - +
343P GLU* 2.6 53.5 + - - +
346P ASN* 3.7 4.0 - - - +
429P MET* 3.8 14.1 - - + -
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Residues in contact with ALA 129 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125P LEU 2.6 20.7 + - - +
126P LEU* 3.0 9.4 + - - +
128P ARG* 1.3 70.7 - - - +
130P ALA* 1.3 69.1 + - - +
132P ARG* 2.9 3.1 + - - +
133P LEU* 2.8 26.9 + - - +
429P MET* 3.8 8.5 - - + +
432P ALA* 4.1 6.5 - - + -
433P CYS* 4.0 31.2 - - - +
436P LEU* 3.7 14.1 - - + -
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Residues in contact with ALA 130 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126P LEU 2.7 13.1 + - - +
127P PHE 3.2 10.1 - - - +
129P ALA* 1.3 77.1 - - - +
131P VAL* 1.3 61.9 + - - +
133P LEU 3.5 0.2 + - - -
134P MET* 3.0 29.3 + - - +
404P LEU* 3.5 21.1 - - + +
408P ILE* 3.7 25.1 - - + -
436P LEU* 3.3 11.4 - - - +
440P TRP* 3.8 11.7 - - + -
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Residues in contact with VAL 131 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127P PHE 3.0 18.2 + - - +
128P ARG* 3.6 7.4 - - - +
129P ALA 3.1 0.4 - - - -
130P ALA* 1.3 76.2 - - - +
132P ARG* 1.3 64.1 + - - +
135P PHE* 2.9 32.5 + - + +
339P LEU* 4.7 1.8 - - + -
340P ILE* 3.8 37.7 - - + +
343P GLU* 3.9 16.4 - - + -
344P LEU* 3.9 25.4 - - + -
347P MET* 3.8 16.2 - - - -
404P LEU* 4.2 10.1 - - + -
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Residues in contact with ARG 132 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128P ARG 3.1 12.4 + - - +
129P ALA 2.9 6.3 + - - +
131P VAL* 1.3 77.0 - - - +
133P LEU* 1.3 61.4 + - + +
136P SER* 2.8 30.7 + - - -
343P GLU* 2.2 37.2 + - + +
346P ASN* 4.0 8.5 + - - +
347P MET* 3.3 56.0 + - + +
429P MET* 3.2 28.8 - - - +
433P CYS* 4.2 16.2 - - - -
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Residues in contact with LEU 133 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129P ALA 2.8 20.0 + - - +
130P ALA 4.0 0.2 - - - +
132P ARG* 1.3 74.5 - - + +
134P MET* 1.3 57.3 + - - +
136P SER* 3.1 15.1 + - - +
293P LYS* 3.1 20.1 - - - -
297P LYS* 5.5 1.8 - - - +
298P TYR* 3.4 25.3 - - + +
433P CYS* 3.9 23.6 - - + +
436P LEU* 3.7 21.8 - - + -
437P ASP* 3.4 40.4 - - + +
440P TRP* 3.7 19.7 - - + -
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Residues in contact with MET 134 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130P ALA 3.0 18.2 + - - +
133P LEU* 1.3 78.2 - - - +
135P PHE* 1.3 75.8 + - + +
136P SER 3.3 2.8 + - - -
138P LEU* 3.6 16.1 - - - +
290P VAL* 3.7 19.2 - - + +
293P LYS* 4.1 4.9 - - - +
294P ILE* 3.9 43.1 - - + -
302P PHE* 4.5 3.4 - - + -
400P LEU* 4.8 9.9 - - + +
403P THR* 4.2 21.3 - - + -
404P LEU* 3.2 37.2 - - + +
440P TRP* 3.9 19.7 - - + -
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Residues in contact with PHE 135 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131P VAL* 2.9 31.8 + - + +
134P MET* 1.3 96.6 - - + +
136P SER* 1.3 62.1 + - - +
138P LEU* 3.9 6.9 - - - +
286P VAL* 4.5 10.1 - - + -
287P ALA* 6.2 0.4 - - - -
290P VAL* 3.8 26.0 - - + -
340P ILE* 5.1 4.9 - - + -
344P LEU* 3.6 37.5 - - + -
347P MET* 3.6 7.0 - - + +
349P TYR* 2.6 46.3 + + + +
353P TRP* 4.7 7.2 - + - -
357P PHE* 5.2 7.0 - + - -
397P ALA* 6.4 0.9 - - + -
400P LEU* 5.3 5.8 - - + -
401P MET* 4.6 21.8 - - + -
404P LEU* 5.1 2.9 - - + -
663P PRO* 5.3 0.3 - - - +
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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
------------------------------------------------------------
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