Contacts of the helix formed by residues 120 - 135 (chain Q) 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 Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118Q PRO* 4.2 2.7 - - - +
119Q VAL* 1.3 84.7 - - - +
121Q GLU* 1.3 64.6 + - - +
122Q ARG* 3.1 15.5 + - - +
123Q ASP* 3.1 30.2 + - - +
124Q ASN* 3.1 19.3 + - - +
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Residues in contact with GLU 121 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120Q SER* 1.3 73.6 - - - +
122Q ARG* 1.3 61.8 + - - +
124Q ASN* 3.2 28.4 + - - +
125Q LEU* 2.9 43.9 + - + +
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Residues in contact with ARG 122 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120Q SER* 3.1 12.1 + - - +
121Q GLU* 1.3 78.6 - - - +
123Q ASP* 1.3 84.1 + - - +
125Q LEU* 2.9 14.2 + - - +
126Q LEU* 2.8 32.2 + - + +
412Q VAL* 3.7 6.4 - - - +
415Q LEU* 3.5 31.3 - - - +
416Q ASP* 2.6 35.3 + - - +
423Q ASN* 2.5 47.9 + - - +
426Q ILE* 4.1 24.5 - - + +
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Residues in contact with ASP 123 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118Q PRO* 4.3 2.5 - - + -
119Q VAL* 4.2 5.7 - - - +
120Q SER* 3.1 16.7 + - - +
122Q ARG* 1.3 104.1 + - - +
124Q ASN* 1.3 64.0 + - - +
126Q LEU* 3.2 8.5 + - - +
127Q PHE* 3.0 35.9 + - + -
412Q VAL* 3.5 21.1 - - + +
416Q ASP* 5.2 0.5 - - - +
484Q PRO* 5.0 1.0 - - - +
485Q TYR* 2.5 41.6 + - + +
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Residues in contact with ASN 124 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118Q PRO* 3.7 24.3 - - + +
120Q SER 3.1 10.2 + - - +
121Q GLU* 3.2 35.8 + - - +
122Q ARG 3.1 0.2 - - - -
123Q ASP* 1.3 75.6 - - - +
125Q LEU* 1.3 64.4 + - - +
127Q PHE* 3.5 2.4 + - - +
128Q ARG* 2.8 57.9 + - - +
339Q LEU* 3.9 9.5 - - - +
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Residues in contact with LEU 125 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121Q GLU* 2.9 39.5 + - + +
122Q ARG* 2.9 10.8 + - - +
124Q ASN* 1.3 79.2 - - - +
126Q LEU* 1.3 50.4 + - - +
128Q ARG* 3.2 5.1 + - - +
129Q ALA* 2.6 38.1 + - - +
426Q ILE* 4.4 14.4 - - + +
427Q LYS 3.9 8.1 - - - +
428Q ASP* 3.8 28.0 - - - +
429Q MET* 3.5 40.1 - - + +
432Q ALA* 4.2 9.9 - - + -
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Residues in contact with LEU 126 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122Q ARG* 2.8 37.3 + - + +
123Q ASP 3.2 6.5 + - - +
125Q LEU* 1.3 73.7 - - - +
127Q PHE* 1.3 51.8 + - - +
129Q ALA* 3.0 4.6 + - - +
130Q ALA* 2.7 34.5 + - - +
408Q ILE* 3.8 18.8 - - + +
411Q LEU* 3.9 22.0 - - + -
412Q VAL* 4.1 17.7 - - + -
415Q LEU* 3.9 21.1 - - + -
426Q ILE* 4.2 24.2 - - + -
432Q ALA* 5.0 4.9 - - + +
435Q PHE* 4.4 7.6 - - + -
436Q LEU* 3.9 13.4 - - + +
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Residues in contact with PHE 127 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118Q PRO* 4.3 13.2 - - + -
123Q ASP* 3.0 29.9 + - + +
124Q ASN 3.9 3.4 - - - +
126Q LEU* 1.3 75.6 - - - +
128Q ARG* 1.3 59.2 + - - +
130Q ALA* 3.1 6.8 + - - +
131Q VAL* 3.0 28.2 + - - +
335Q TRP* 3.7 26.9 - + - -
336Q LEU* 4.0 18.6 - - + -
339Q LEU* 3.9 17.0 - - + -
404Q LEU* 4.4 7.9 - - + +
405Q LEU* 4.0 21.8 - - + -
408Q ILE* 3.5 36.6 - - + -
409Q THR* 4.5 5.2 - - - -
485Q TYR* 4.1 33.9 - + - -
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Residues in contact with ARG 128 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124Q ASN* 2.8 44.7 + - - +
125Q LEU* 3.6 5.6 - - - +
127Q PHE* 1.3 76.5 - - - +
129Q ALA* 1.3 65.2 + - - +
131Q VAL* 3.4 1.4 + - - +
132Q ARG* 3.1 27.2 + - - +
339Q LEU* 3.5 31.1 - - + +
342Q ASP* 2.9 33.7 + - - +
343Q GLU* 2.6 52.3 + - - +
346Q ASN* 3.7 4.8 - - - +
429Q MET* 3.8 13.9 - - + -
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Residues in contact with ALA 129 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125Q LEU 2.6 20.2 + - - +
126Q LEU* 3.3 9.4 - - - +
128Q ARG* 1.3 71.4 - - - +
130Q ALA* 1.3 68.9 + - - +
132Q ARG* 2.9 3.1 + - - +
133Q LEU* 2.8 26.0 + - - +
429Q MET* 3.8 8.9 - - + +
432Q ALA* 4.1 6.7 - - + -
433Q CYS* 4.0 31.4 - - - +
436Q LEU* 3.7 14.8 - - + -
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Residues in contact with ALA 130 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126Q LEU 2.7 12.9 + - - +
127Q PHE 3.2 10.1 - - - +
129Q ALA* 1.3 76.8 - - - +
131Q VAL* 1.3 62.8 + - - +
133Q LEU 4.0 0.3 - - - -
134Q MET* 3.0 29.3 + - - +
404Q LEU* 3.5 20.0 - - + +
408Q ILE* 3.7 25.4 - - + -
436Q LEU* 3.3 10.1 - - - +
440Q TRP* 3.8 11.6 - - + -
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Residues in contact with VAL 131 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127Q PHE 3.0 18.3 + - - +
128Q ARG* 3.6 7.4 - - - +
129Q ALA 3.1 0.2 - - - -
130Q ALA* 1.3 76.4 - - - +
132Q ARG* 1.3 64.7 + - - +
135Q PHE* 2.9 32.3 + - + +
339Q LEU* 4.7 1.8 - - + -
340Q ILE* 3.8 37.9 - - + +
343Q GLU* 3.9 16.4 - - + -
344Q LEU* 3.9 24.7 - - + -
347Q MET* 3.8 16.6 - - - -
404Q LEU* 4.2 11.4 - - + -
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Residues in contact with ARG 132 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128Q ARG 3.1 11.5 + - - +
129Q ALA 2.9 6.5 + - - +
131Q VAL* 1.3 77.3 - - - +
133Q LEU* 1.3 59.8 + - + +
136Q SER* 2.8 30.7 + - - -
343Q GLU* 2.2 36.3 + - - +
346Q ASN* 4.0 9.1 + - - +
347Q MET* 3.3 54.9 - - + +
429Q MET* 3.2 29.1 - - - +
433Q CYS* 4.2 16.2 - - - -
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Residues in contact with LEU 133 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129Q ALA 2.8 19.8 + - - +
132Q ARG* 1.3 72.8 - - - +
134Q MET* 1.3 57.7 + - - +
136Q SER* 3.1 15.1 + - - +
293Q LYS* 3.1 19.8 - - - -
297Q LYS* 5.5 2.0 - - - +
298Q TYR* 3.4 23.6 - - + +
433Q CYS* 3.9 24.0 - - + +
436Q LEU* 3.7 20.4 - - + -
437Q ASP* 3.4 41.1 - - + +
440Q TRP* 3.7 20.2 - - + -
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Residues in contact with MET 134 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130Q ALA 3.0 16.9 + - - +
133Q LEU* 1.3 80.1 - - - +
135Q PHE* 1.3 77.4 + - + +
136Q SER 3.3 2.9 + - - -
138Q LEU* 3.6 15.9 - - - +
290Q VAL* 3.7 18.7 - - + +
293Q LYS* 4.1 4.9 - - - +
294Q ILE* 3.9 43.1 - - + -
302Q PHE* 4.5 3.4 - - + -
400Q LEU* 4.8 10.1 - - + +
401Q MET* 6.4 0.2 - - - -
403Q THR* 4.2 20.4 - - + -
404Q LEU* 3.2 37.7 - - + +
440Q TRP* 3.9 20.2 - - + -
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Residues in contact with PHE 135 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131Q VAL* 2.9 32.2 + - + +
134Q MET* 1.3 95.9 - - + +
136Q SER* 1.3 62.0 + - - +
138Q LEU* 3.9 7.6 - - - +
286Q VAL* 4.5 10.3 - - + -
287Q ALA* 6.2 0.9 - - - -
290Q VAL* 3.8 26.2 - - + -
340Q ILE* 5.1 5.2 - - + -
344Q LEU* 3.6 37.5 - - + -
347Q MET* 3.6 6.4 - - + +
349Q TYR* 2.6 45.5 + + + +
353Q TRP* 4.7 7.4 - + - -
357Q PHE* 5.2 6.1 - + - -
397Q ALA* 6.4 0.9 - - + -
400Q LEU* 5.3 5.8 - - + -
401Q MET* 4.6 22.7 - - + -
404Q LEU* 5.1 2.7 - - + -
663Q 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
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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