Contacts of the helix formed by residues 160 - 171 (chain I) in PDB entry 3J7Y
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 LYS 160 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115I GLN* 3.6 24.7 - - - +
116I LEU* 4.2 7.1 - - + +
118I LYS* 4.9 6.7 - - - +
119I HIS* 3.4 49.3 + - + +
121I ILE* 3.7 17.7 - - + +
156I SER* 4.1 1.2 + - - -
158I GLU 3.5 2.4 + - - -
159I PRO* 1.3 74.6 - - - +
161I VAL* 1.3 65.0 + - - +
162I LYS* 3.2 4.9 - - + +
163I GLU* 3.4 53.8 + - + +
164I MET* 3.8 3.6 + - - +
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Residues in contact with VAL 161 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95I MET* 3.5 25.4 - - + -
97I ALA* 3.7 16.4 - - + -
121I ILE* 3.6 21.8 - - + -
154I LEU* 4.5 4.5 - - + -
159I PRO* 5.7 0.4 - - + -
160I LYS* 1.3 75.4 - - - +
162I LYS* 1.3 61.6 + - - +
163I GLU 3.2 0.7 - - - -
164I MET* 3.2 9.6 + - + +
165I VAL* 2.9 33.4 + - + +
176I LEU* 5.0 4.2 - - + +
191I PHE* 3.7 22.2 - - + -
194I TYR* 3.5 33.9 - - + -
195I SER* 5.4 0.9 - - - +
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Residues in contact with LYS 162 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160I LYS* 3.2 4.2 - - + -
161I VAL* 1.3 84.0 - - + +
163I GLU* 1.3 58.3 + - - +
165I VAL* 3.2 10.5 + - - +
166I ARG* 2.9 41.2 + - + +
194I TYR* 5.8 1.1 - - + +
195I SER* 2.8 42.3 + - - +
196I LYS* 4.3 8.2 + - - +
197I LEU 4.4 9.0 - - - +
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Residues in contact with GLU 163 (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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115I GLN* 3.1 36.9 + - + +
116I LEU* 4.7 1.6 - - + -
160I LYS* 3.4 49.9 + - + +
161I VAL 3.2 0.4 - - - -
162I LYS* 1.3 79.0 - - - +
164I MET* 1.3 57.8 + - - +
166I ARG* 3.2 12.1 + - - +
167I ILE* 2.9 48.5 + - + +
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Residues in contact with MET 164 (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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99I CYS* 4.0 21.3 - - + -
101I ASN* 3.2 27.1 - - - +
112I MET* 3.5 31.4 - - + -
116I LEU* 4.4 5.3 - - + +
121I ILE* 6.3 0.4 - - + -
123I MET* 3.6 13.5 - - + -
154I LEU* 3.5 38.8 - - + -
160I LYS 3.8 3.6 + - - +
161I VAL* 3.2 18.1 + - - +
163I GLU* 1.3 77.2 - - - +
165I VAL* 1.3 58.2 + - + +
167I ILE* 3.2 2.4 + - - +
168I LEU* 2.9 51.1 + - + +
175I PRO* 5.2 0.7 - - + -
176I LEU* 5.2 2.7 - - + -
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Residues in contact with VAL 165 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161I VAL 2.9 19.7 + - - +
162I LYS* 3.2 8.3 + - - +
164I MET* 1.3 76.0 - - - +
166I ARG* 1.3 57.2 + - + +
168I LEU* 3.2 8.9 + - + +
169I ARG* 2.9 64.8 + - + +
174I LEU* 5.9 5.6 - - + -
176I LEU* 3.7 34.5 - - + -
191I PHE* 5.1 2.9 - - + -
192I ILE* 5.9 2.5 - - + -
195I SER* 3.4 26.7 - - - +
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Residues in contact with ARG 166 (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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162I LYS* 2.9 30.5 + - + +
163I GLU* 3.4 16.6 - - - +
165I VAL* 1.3 77.2 - - + +
167I ILE* 1.3 59.1 + - + +
169I ARG* 3.2 40.7 + - - +
170I THR* 2.9 32.4 + - - +
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Residues in contact with ILE 167 (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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104I LEU* 5.7 2.0 - - + -
108I ASP 5.9 0.7 - - - +
111I LEU* 5.6 2.5 - - + -
112I MET* 3.4 40.8 - - + +
115I GLN* 3.6 39.5 - - + +
163I GLU* 2.9 31.1 + - + +
164I MET 3.2 6.7 + - - +
166I ARG* 1.3 78.0 - - + +
168I LEU* 1.3 64.7 + - + +
170I THR* 3.0 22.8 + - + +
171I VAL* 3.0 24.4 + - + +
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Residues in contact with LEU 168 (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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101I ASN* 5.3 2.5 - - - +
104I LEU* 5.0 13.0 - - + -
112I MET* 4.5 8.3 - - - -
164I MET* 2.9 47.5 + - + +
165I VAL* 3.5 11.7 - - - +
167I ILE* 1.3 77.5 - - + +
169I ARG* 1.3 54.1 + - - +
171I VAL* 2.6 47.5 + - + +
172I PRO 3.3 0.5 - - - -
173I PHE* 3.5 36.6 + - + +
174I LEU* 6.1 0.7 - - + -
175I PRO* 3.4 40.4 - - + -
176I LEU* 4.8 2.0 - - + -
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Residues in contact with ARG 169 (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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165I VAL* 2.9 49.1 + - + +
166I ARG* 3.3 40.7 - - - +
168I LEU* 1.3 76.8 - - + +
170I THR* 1.3 62.4 + - - +
171I VAL 3.3 0.5 + - - -
172I PRO* 3.8 14.4 - - - +
173I PHE 4.6 2.0 + - - +
174I LEU* 5.6 9.6 - - + +
192I ILE* 3.8 32.6 + - - +
195I SER* 4.5 8.1 - - - -
196I LYS* 5.6 1.6 - - - +
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Residues in contact with THR 170 (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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166I ARG* 2.9 18.8 + - - +
167I ILE* 3.0 25.8 + - + +
169I ARG* 1.3 76.4 - - - +
171I VAL* 1.3 69.5 + - + +
172I PRO* 3.7 6.6 - - - +
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Residues in contact with VAL 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104I LEU* 3.9 28.0 - - + -
108I ASP* 5.0 9.9 - - - +
167I ILE* 3.0 21.0 + - + +
168I LEU* 2.6 28.5 + - + +
170I THR* 1.3 85.7 - - + +
172I PRO* 1.3 55.2 - - - -
173I PHE* 2.6 27.9 + - + +
40k GLU* 4.5 10.1 - - - +
43k ARG* 4.0 15.5 - - - +
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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