Contacts of the helix formed by residues 118 - 126 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114L PHE* 3.3 52.4 + + - +
115L ILE 4.0 3.6 - - - -
116L ASP 3.4 0.2 - - - -
117L GLN* 1.3 102.2 + - + +
119L ARG* 1.3 57.0 + - - +
120L ALA 3.3 2.5 - - - -
121L ALA* 3.2 8.7 + - + +
122L LEU* 2.9 31.2 + - + +
192L LEU* 3.3 54.9 + - + +
193L GLU* 5.2 0.4 - - - -
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Residues in contact with ARG 119 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134I ASP* 3.8 9.8 + - - -
137I TYR* 3.2 55.9 + - + -
143I ASP* 5.5 0.8 + - - -
146I TYR* 3.3 37.4 + - - -
115L ILE 3.8 9.8 + - - +
116L ASP* 3.9 16.6 - - - +
117L GLN 3.4 4.2 + - - -
118L HIS* 1.3 77.5 - - - +
120L ALA* 1.3 63.0 + - - +
123L ILE* 3.2 48.8 + - - +
160L ARG* 4.6 6.7 + - - +
163L PHE* 3.7 51.8 + - + +
164L SER* 5.7 0.6 - - - +
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Residues in contact with ALA 120 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I TRP* 5.1 10.5 + - + +
134I ASP* 3.9 37.9 + - + +
135I ALA* 4.8 4.3 - - + +
117L GLN 5.2 0.2 + - - -
118L HIS 3.3 0.4 - - - -
119L ARG* 1.3 79.1 - - - +
121L ALA* 1.3 60.6 + - - +
123L ILE* 3.9 3.3 + - - +
124L ALA* 3.6 21.7 + - - +
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Residues in contact with ALA 121 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118L HIS* 3.2 16.1 + - + +
120L ALA* 1.3 79.2 - - - +
122L LEU* 1.3 60.9 + - - +
123L ILE 3.2 0.4 - - - -
124L ALA* 5.1 2.0 - - - -
125L ARG* 3.0 43.4 + - - +
188L LEU* 5.4 0.7 - - - +
192L LEU* 4.2 28.5 - - + -
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Residues in contact with LEU 122 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114L PHE* 4.4 9.0 - - + +
115L ILE* 4.1 34.5 - - + +
118L HIS* 2.9 20.6 + - + +
119L ARG 4.4 0.2 - - - +
120L ALA 3.5 0.2 - - - -
121L ALA* 1.3 73.5 - - - +
123L ILE* 1.3 64.2 + - - +
126L VAL* 3.2 42.9 - - + +
159L MET* 3.3 12.1 - - + +
163L PHE* 3.7 27.4 - - + -
177L LEU* 5.6 0.9 - - + -
181L LEU* 4.0 17.3 - - + -
188L LEU* 4.3 10.1 - - + -
189L VAL* 6.1 0.7 - - + -
192L LEU* 3.9 22.2 - - + -
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Residues in contact with ILE 123 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I TRP* 6.2 0.4 - - + -
134I ASP* 3.4 30.7 - - - +
119L ARG* 3.2 39.0 + - - +
120L ALA 4.2 4.3 - - - +
121L ALA 3.2 0.6 - - - -
122L LEU* 1.3 80.8 - - - +
124L ALA* 1.3 64.4 + - + +
125L ARG 3.4 0.5 + - - -
126L VAL 4.2 4.5 + - - +
156L PRO* 3.3 41.6 - - + +
159L MET* 3.8 11.3 - - + +
160L ARG* 3.7 36.6 - - + +
163L PHE* 3.8 16.8 - - + -
144M GLU* 5.4 0.2 - - - +
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Residues in contact with ALA 124 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I TRP* 4.9 7.6 - - + +
120L ALA 3.6 13.7 + - - +
121L ALA* 3.5 2.7 + - - -
123L ILE* 1.3 81.4 - - + +
125L ARG* 1.3 69.1 + - + +
126L VAL 3.8 1.8 - - - +
127L THR* 5.3 1.9 - - - +
156L PRO* 4.4 9.3 - - - +
143M ASP* 4.7 5.9 - - - +
144M GLU* 2.8 30.4 - - - +
147M GLN* 5.9 0.7 + - - -
167P PRO* 3.9 12.5 - - - +
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Residues in contact with ARG 125 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121L ALA* 3.0 23.6 + - - +
124L ALA* 1.3 90.0 - - + +
126L VAL* 1.3 55.1 + - - +
127L THR* 4.5 0.9 - - - -
188L LEU* 3.3 25.4 - - + +
191L ASP* 3.7 20.1 + - - +
192L LEU* 3.3 31.7 - - - +
167P PRO* 2.8 28.5 + - + +
168P ALA* 2.7 37.7 - - - +
169P TRP 2.9 32.7 + - - -
170P ASN* 4.3 0.6 - - - +
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Residues in contact with VAL 126 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122L LEU* 3.2 39.6 + - + +
123L ILE 4.2 6.6 + - - +
124L ALA 3.8 0.7 - - - -
125L ARG* 1.3 76.4 + - - +
127L THR* 1.3 64.6 + - - +
128L ASN* 3.9 8.7 - - + +
129L VAL* 3.7 25.1 - - + +
132L LEU* 5.0 3.6 - - + -
155L ASN* 3.9 15.8 + - - +
156L PRO* 5.9 0.5 - - - +
159L MET* 3.9 17.2 - - + +
181L LEU* 4.2 17.9 - - + -
185L GLN* 5.3 3.4 - - + +
188L LEU* 3.7 20.6 - - + -
168P ALA* 4.4 0.4 - - - -
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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