Contacts of the helix formed by residues 118 - 126 (chain I) in PDB entry 6N1H
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 HIS 118 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114I PHE* 3.3 52.4 + + - +
115I ILE 4.0 3.6 - - - -
116I ASP 3.4 0.2 - - - -
117I GLN* 1.3 100.9 + - + +
119I ARG* 1.3 57.5 + - - +
120I ALA 3.3 2.9 - - - -
121I ALA* 3.2 9.5 + - + +
122I LEU* 2.9 30.7 + - + +
192I LEU* 3.3 54.6 + - + +
193I GLU* 5.2 0.6 - - - -
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Residues in contact with ARG 119 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F ASP* 3.9 8.5 + - - -
137F TYR* 3.2 56.6 + - + -
143F ASP* 5.4 1.2 + - - -
146F TYR* 3.3 38.2 + - - -
115I ILE 3.8 10.2 + - - +
116I ASP* 3.9 15.7 - - - +
117I GLN 3.4 4.4 + - - -
118I HIS* 1.3 77.1 - - - +
120I ALA* 1.3 63.9 + - - +
122I LEU 3.7 0.2 + - - -
123I ILE* 3.3 49.1 + - - +
160I ARG 4.6 6.3 + - - -
163I PHE* 3.7 51.8 + - + +
164I SER* 5.1 0.8 - - - +
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Residues in contact with ALA 120 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F TRP* 5.2 10.9 + - + +
134F ASP* 3.8 38.2 + - + +
135F ALA* 4.8 3.8 - - + +
117I GLN 5.2 0.4 + - - -
118I HIS 3.3 0.2 - - - -
119I ARG* 1.3 80.0 - - - +
121I ALA* 1.3 60.6 + - - +
123I ILE* 3.9 3.4 + - - +
124I ALA* 3.6 20.8 + - - +
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Residues in contact with ALA 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118I HIS* 3.2 14.8 + - + +
120I ALA* 1.3 79.2 - - - +
122I LEU* 1.3 60.9 + - - +
123I ILE 3.2 0.4 - - - -
124I ALA* 3.5 1.7 + - - -
125I ARG* 3.0 42.5 + - - +
188I LEU* 5.4 0.3 - - - +
192I LEU* 4.2 28.7 - - + -
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Residues in contact with LEU 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114I PHE* 4.4 9.2 - - + +
115I ILE* 4.1 33.7 - - + +
118I HIS* 2.9 21.3 + - + +
119I ARG 3.7 0.2 + - - -
121I ALA* 1.3 74.7 - - - +
123I ILE* 1.3 64.6 + - - +
125I ARG 4.3 0.4 - - - -
126I VAL* 3.2 42.9 - - + +
159I MET* 3.3 12.4 - - + +
163I PHE* 3.7 27.4 - - + -
177I LEU* 5.6 0.4 - - + -
181I LEU* 4.0 17.9 - - + -
188I LEU* 4.3 9.6 - - + -
189I VAL* 6.1 1.1 - - + -
192I LEU* 3.9 21.5 - - + -
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Residues in contact with ILE 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F TRP* 6.3 0.4 - - + -
134F ASP* 3.4 30.3 - - + +
119I ARG* 3.3 37.9 + - - +
120I ALA 4.2 4.3 - - - +
121I ALA 3.2 0.4 - - - -
122I LEU* 1.3 80.7 - - - +
124I ALA* 1.3 65.7 + - + +
125I ARG 3.4 0.5 + - - -
126I VAL 4.2 4.3 + - - +
156I PRO* 3.3 42.3 - - + +
159I MET* 3.8 10.6 - - + +
160I ARG* 3.7 37.7 - - + +
163I PHE* 3.8 17.5 - - + -
144J GLU* 5.3 0.2 - - - +
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Residues in contact with ALA 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F TRP* 4.9 7.9 - - + +
120I ALA 3.6 13.8 + - - +
121I ALA* 3.5 2.0 + - - -
123I ILE* 1.3 81.4 - - + +
125I ARG* 1.3 70.2 + - + +
126I VAL 3.8 1.8 - - - +
127I THR* 5.3 2.1 - - - +
156I PRO* 4.4 9.7 - - - +
143J ASP* 4.7 5.9 - - - +
144J GLU* 2.8 29.8 - - - +
147J GLN* 5.9 0.9 + - - -
167M PRO* 3.9 12.3 - - - +
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Residues in contact with ARG 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121I ALA* 3.0 21.4 + - - +
124I ALA* 1.3 91.6 - - + +
126I VAL* 1.3 53.2 - - - +
127I THR* 4.5 1.1 - - - -
188I LEU* 3.3 26.5 - - + +
191I ASP* 3.7 20.7 + - - +
192I LEU* 3.3 31.3 - - - +
167M PRO* 2.8 28.3 + - + +
168M ALA* 2.7 37.5 - - - +
169M TRP 2.9 32.3 + - - -
170M ASN* 4.3 0.6 - - - +
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Residues in contact with VAL 126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122I LEU* 3.2 39.4 + - + +
123I ILE 4.5 6.1 - - - +
124I ALA 3.8 0.9 - - - -
125I ARG* 1.3 74.8 - - - +
127I THR* 1.3 65.1 + - - +
128I ASN* 3.9 10.1 - - + +
129I VAL* 3.7 24.7 - - + +
132I LEU* 5.0 3.4 - - + -
155I ASN* 3.9 16.1 + - - +
156I PRO* 5.9 0.2 - - - +
159I MET* 3.9 16.7 - - + +
181I LEU* 4.2 19.3 - - + -
185I GLN* 5.3 3.4 - - - +
188I LEU* 3.7 21.1 - - + -
168M ALA* 4.4 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