Contacts of the helix formed by residues 118 - 126 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114O PHE* 3.3 52.4 + + - +
115O ILE 4.0 3.8 - - - -
116O ASP 3.4 0.2 - - - -
117O GLN* 1.3 99.3 + - + +
119O ARG* 1.3 57.4 + - - +
120O ALA 3.3 3.4 - - - -
121O ALA* 3.2 9.7 + - + +
122O LEU* 2.9 30.8 + - + +
192O LEU* 3.3 55.2 + - + +
193O GLU* 5.2 0.6 - - - -
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Residues in contact with ARG 119 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134L ASP* 3.8 8.5 + - - -
137L TYR* 3.2 56.6 + - + -
143L ASP* 5.5 1.0 + - - -
146L TYR* 3.3 37.9 + - - -
115O ILE 3.8 9.4 + - - +
116O ASP* 3.9 15.7 - - - +
117O GLN 3.4 4.4 + - - -
118O HIS* 1.3 77.1 - - - +
120O ALA* 1.3 63.0 + - - +
122O LEU 3.7 0.2 + - - -
123O ILE* 3.3 49.0 + - - +
160O ARG* 4.6 6.5 + - - +
163O PHE* 3.7 52.3 + - + +
164O SER* 5.7 0.4 - - - +
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Residues in contact with ALA 120 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131L TRP* 5.2 10.9 + - + +
134L ASP* 3.9 37.7 + - + +
135L ALA* 4.8 3.8 - - - +
117O GLN 5.2 0.4 + - - -
118O HIS 3.3 0.2 - - - -
119O ARG* 1.3 79.6 - - - +
121O ALA* 1.3 59.9 + - - +
123O ILE* 3.9 2.9 + - - +
124O ALA* 3.6 20.8 + - - +
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Residues in contact with ALA 121 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118O HIS* 3.2 15.0 + - + +
120O ALA* 1.3 79.2 - - - +
122O LEU* 1.3 60.7 + - - +
123O ILE 3.2 0.2 - - - -
124O ALA* 5.1 1.8 - - - -
125O ARG* 3.0 42.8 + - - +
188O LEU* 5.4 0.3 - - - +
192O LEU* 4.2 29.2 - - + -
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Residues in contact with LEU 122 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114O PHE* 4.4 9.0 - - + +
115O ILE* 4.1 34.1 - - + +
118O HIS* 2.9 20.0 + - + +
121O ALA* 1.3 75.4 - - - +
123O ILE* 1.3 65.4 + - - +
125O ARG 4.3 0.2 - - - -
126O VAL* 3.2 43.7 - - + +
159O MET* 3.3 12.5 - - + +
163O PHE* 3.7 27.1 - - + -
177O LEU* 5.6 0.2 - - + -
181O LEU* 4.0 18.2 - - + -
188O LEU* 4.3 9.4 - - + -
189O VAL* 6.1 0.9 - - + -
192O LEU* 3.9 21.8 - - + -
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Residues in contact with ILE 123 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131L TRP* 6.2 0.4 - - + -
134L ASP* 3.4 24.0 - - + +
119O ARG* 3.3 45.1 + - - +
120O ALA 4.2 4.5 - - - +
121O ALA 3.2 0.8 - - - -
122O LEU* 1.3 81.6 - - - +
124O ALA* 1.3 66.0 + - + +
125O ARG 3.4 0.3 + - - -
126O VAL 4.2 4.3 + - - +
156O PRO* 3.3 41.8 - - + +
159O MET* 3.8 10.4 - - + +
160O ARG* 3.7 37.0 - - + +
163O PHE* 3.8 17.3 - - + -
144P GLU* 5.4 0.2 - - - +
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Residues in contact with ALA 124 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131L TRP* 4.9 7.2 - - + +
120O ALA 3.6 13.8 + - - +
121O ALA* 3.5 2.6 + - - -
123O ILE* 1.3 80.7 - - + +
125O ARG* 1.3 69.8 + - + +
126O VAL 3.8 1.8 - - - +
127O THR* 5.3 4.2 - - - +
156O PRO* 4.4 9.3 - - - +
143P ASP* 4.6 12.5 - - - +
144P GLU* 2.8 30.0 - - - +
147P GLN* 5.8 1.0 + - - -
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Residues in contact with ARG 125 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121O ALA* 3.0 22.8 + - - +
124O ALA* 1.3 90.1 - - + +
126O VAL* 1.3 61.7 + - - +
127O THR* 3.7 11.2 + - - +
185O GLN* 4.8 2.4 + - - -
187O TYR* 6.2 1.2 - - - -
188O LEU* 3.3 39.6 - - + +
191O ASP* 3.7 24.1 + - - +
192O LEU* 3.3 31.1 - - - +
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Residues in contact with VAL 126 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121O ALA 4.3 0.2 + - - -
122O LEU* 3.2 38.8 + - + +
123O ILE 4.5 6.2 - - - +
124O ALA 5.1 0.7 - - - -
125O ARG* 1.3 76.3 - - - +
127O THR* 1.3 64.8 + - - +
128O ASN* 3.9 10.1 - - + +
129O VAL* 3.7 24.6 - - + +
132O LEU* 5.0 4.0 - - + -
155O ASN* 3.9 16.3 + - - +
156O PRO* 5.9 0.2 - - - +
159O MET* 3.9 15.7 - - + +
181O LEU* 4.2 18.4 - - + -
185O GLN* 5.3 3.4 - - - +
188O LEU* 3.7 21.3 - - + -
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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