Contacts of the helix formed by residues 160 - 170 (chain A) in PDB entry 3F98
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 TYR 160 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A TYR* 4.3 5.1 + - - -
149A PHE* 3.3 39.3 - + + -
151A HIS* 3.5 27.8 - - + -
152A GLY* 3.1 16.3 + - - -
155A ALA* 3.8 16.3 - - + +
156A PHE 4.3 3.6 - - - -
157A ARG 4.5 5.2 + - - +
158A THR 3.3 1.2 - - - -
159A LEU* 1.3 85.5 - - + +
161A SER* 1.3 59.9 + - - +
162A ALA 3.3 2.5 - - - -
163A ILE* 3.4 8.2 + - + +
164A GLY* 2.9 23.4 + - - -
272A HIS* 2.7 47.3 + + + -
354A PHE 3.5 19.1 - - - -
355A ALA* 3.7 18.5 - - + +
356A ASP* 3.7 3.1 - - - -
473A NTJ 3.9 3.1 - - - +
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Residues in contact with SER 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ILE* 3.6 3.7 - - - +
84A TYR* 3.4 26.8 + - - -
97A TRP* 4.2 0.5 - - - -
130A THR* 2.7 35.2 + - - -
158A THR 4.1 5.2 - - - -
160A TYR* 1.3 74.1 - - - +
162A ALA* 1.3 61.9 + - - +
163A ILE 3.1 0.7 - - - -
164A GLY 4.1 0.2 - - - +
165A ILE* 2.8 42.8 + - - +
356A ASP* 2.6 23.2 + - - -
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Residues in contact with ALA 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ILE* 4.0 13.9 - - + +
57A PRO* 4.1 16.5 - - + +
58A ARG 6.2 0.3 - - - -
161A SER* 1.3 75.7 + - - +
163A ILE* 1.3 62.5 + - + +
165A ILE* 4.5 0.3 - - - +
166A ASP* 3.2 25.1 + - - +
354A PHE 5.8 1.3 - - - +
355A ALA 6.0 0.2 - - - -
356A ASP* 2.9 18.0 + - - +
359A PHE* 3.7 26.7 - - + -
381A ILE* 4.4 12.3 - - + -
385A ASN* 3.9 4.0 + - - -
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Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A PHE* 4.0 29.4 - - + -
160A TYR* 3.4 10.2 + - + +
161A SER 3.1 0.4 - - - -
162A ALA* 1.3 75.3 - - - +
164A GLY* 1.3 65.4 + - - +
166A ASP* 3.2 2.8 + - - +
167A LEU* 3.0 42.0 + - + +
270A ILE* 5.3 3.1 - - + -
295A LEU* 3.7 28.7 - - + -
354A PHE* 3.3 26.0 - - + +
381A ILE* 4.0 17.5 - - + -
384A SER* 5.6 1.3 - - - +
385A ASN* 3.7 23.1 - - - +
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Residues in contact with GLY 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TYR* 3.8 26.6 - - - +
149A PHE* 6.4 0.4 - - - -
160A TYR 2.9 15.7 + - - -
161A SER 3.9 0.7 - - - -
163A ILE* 1.3 78.5 - - - +
165A ILE* 1.3 58.0 + - - +
167A LEU 3.4 0.2 + - - -
168A ALA* 2.9 29.5 + - - +
174A VAL* 3.7 21.0 - - - +
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Residues in contact with ILE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ILE* 5.1 0.7 - - + -
57A PRO 5.0 1.3 - - - +
58A ARG 4.4 2.0 - - - -
59A GLY 3.6 22.7 - - - +
65A VAL* 3.5 19.9 - - + +
84A TYR* 3.8 17.9 - - + -
130A THR* 3.3 27.4 - - + +
131A PRO* 3.7 39.5 - - + +
132A ALA* 4.0 12.1 - - + -
161A SER* 2.8 28.0 + - - +
162A ALA 4.5 1.1 - - - +
164A GLY* 1.3 70.0 - - - -
166A ASP* 1.3 65.6 + - - +
169A SER* 2.8 23.6 + - - -
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Residues in contact with ASP 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A ARG 4.6 0.9 - - - +
59A GLY* 3.5 6.1 - - - -
60A ASN* 2.8 43.6 + - - +
162A ALA 3.2 21.1 + - - +
163A ILE 3.2 2.9 + - - +
165A ILE* 1.3 78.0 - - - +
167A LEU* 1.3 62.2 + - - +
169A SER* 2.8 21.3 + - - -
170A HIS* 2.9 28.4 + - - -
385A ASN* 3.4 37.1 - - - +
386A LYS* 5.9 0.3 - - - +
389A LEU* 4.0 6.2 - - - +
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Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A VAL* 4.3 9.9 - - + -
149A PHE* 5.6 0.9 - - + -
163A ILE* 3.0 38.0 + - + +
166A ASP* 1.3 79.2 - - + +
168A ALA* 1.3 63.1 + - - +
170A HIS* 3.0 13.2 + - - -
172A PHE* 3.2 33.2 + - + -
174A VAL* 3.6 28.0 - - + -
270A ILE* 4.2 18.4 - - + -
385A ASN* 5.6 4.5 - - + +
388A SER* 5.3 6.1 - - - -
389A LEU* 4.0 18.4 - - + -
392A LEU* 3.8 28.0 - - + -
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Residues in contact with ALA 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A TYR* 4.1 2.6 - - - +
65A VAL* 3.6 29.2 - - + -
84A TYR* 4.0 2.9 - - + -
85A TYR 3.7 16.6 - - - +
86A PRO* 3.6 12.5 - - - +
164A GLY 2.9 18.1 + - - +
165A ILE 3.8 0.2 - - - +
167A LEU* 1.3 76.4 - - - +
169A SER* 1.3 57.9 + - - +
170A HIS 3.1 0.2 - - - -
171A GLY* 2.9 20.4 + - - -
172A PHE 3.1 20.4 - - - +
174A VAL* 4.3 1.3 - - + +
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Residues in contact with SER 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLY* 3.4 18.4 - - - -
60A ASN 3.4 0.7 + - - -
61A GLY* 2.8 25.7 + - - -
62A PRO* 3.1 11.1 - - - +
63A TYR* 3.0 49.2 + - - -
65A VAL* 3.4 5.5 - - - +
165A ILE 2.8 14.5 + - - -
166A ASP 2.8 17.2 + - - -
168A ALA* 1.3 75.8 - - - +
170A HIS* 1.3 55.6 + - - +
171A GLY 3.3 0.9 - - - -
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Residues in contact with HIS 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ASN* 3.8 11.2 + - + +
61A GLY* 3.3 28.0 + - - -
62A PRO* 4.5 0.2 - - + -
63A TYR* 4.0 0.4 - - - -
166A ASP* 2.9 40.0 + - - +
167A LEU 3.0 10.7 + - - +
169A SER* 1.3 76.0 + - - +
171A GLY* 1.3 59.3 + - - +
172A PHE* 3.7 2.9 - - + -
386A LYS* 6.3 0.7 - - + -
389A LEU* 3.5 29.0 - - + +
400A LYS* 4.8 3.8 - - - -
402A PHE* 3.7 30.7 - + + -
405A TRP* 4.2 12.7 - + - -
552A FMT 3.1 42.0 - - - +
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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