Contacts of the helix formed by residues 155 - 164 (chain A) in PDB entry 1F5J
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 VAL 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ILE* 3.0 18.4 + - + +
64A ILE* 3.8 29.4 - - + -
80A ILE* 4.1 7.4 - - + -
91A PHE* 5.1 1.1 - - + -
93A ILE* 4.0 17.5 - - + -
153A VAL* 3.2 19.9 - - + +
154A THR* 1.3 70.9 - - - +
156A THR* 1.3 62.0 + - - +
158A HIS* 3.1 14.7 + - - +
159A PHE* 3.1 42.7 + - + -
175A ILE* 4.2 15.7 - - + -
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Residues in contact with THR 156 (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 TRP* 4.7 7.9 - - + +
59A LEU* 4.4 8.5 - - + -
60A GLY 3.4 20.6 - - - +
61A THR* 3.5 7.4 - - - +
62A ILE* 3.1 44.5 + - + +
154A THR* 4.0 6.9 - - - +
155A VAL* 1.3 73.8 - - - +
157A ASP* 1.3 66.1 + - - +
158A HIS 3.3 0.2 - - - -
159A PHE* 3.6 22.8 - - + +
160A ARG* 3.1 22.2 + - - +
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Residues in contact with ASP 157 (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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61A THR* 5.7 0.7 - - - +
113A ILE* 3.7 26.6 - - + +
114A ASP* 5.3 0.9 + - - +
154A THR* 2.8 36.1 + - - +
156A THR* 1.3 77.9 + - - +
158A HIS* 1.3 62.1 + - - +
160A ARG* 3.3 6.7 + - - +
161A ALA* 2.9 27.5 + - - +
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Residues in contact with HIS 158 (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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93A ILE* 3.6 36.0 - - + +
113A ILE* 3.6 36.1 - - + +
114A ASP* 4.4 1.0 + - - -
118A TYR* 3.8 30.3 - + - -
142A SER* 2.8 37.1 + - - +
153A VAL* 4.0 9.1 - - + +
154A THR 3.6 15.0 - - - -
155A VAL 3.1 7.5 + - - +
157A ASP* 1.3 75.5 - - - +
159A PHE* 1.3 65.8 + - - +
161A ALA* 3.1 3.4 + - - +
162A TRP* 2.8 37.1 + - + -
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Residues in contact with PHE 159 (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 TRP* 3.4 35.9 - + + -
59A LEU* 4.2 14.6 - - + -
91A PHE* 3.8 27.8 - + - -
155A VAL* 3.1 34.1 + - + -
156A THR* 3.6 23.1 - - + +
158A HIS* 1.3 77.8 - - - +
160A ARG* 1.3 57.0 + - - +
162A TRP* 3.3 30.5 + + - +
163A ALA* 2.9 29.1 + - - +
167A LEU 4.9 0.5 - - - +
169A LEU* 3.4 21.0 - - + +
172A ILE* 4.0 17.5 - - + -
175A ILE* 4.2 8.5 - - + -
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Residues in contact with ARG 160 (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 TRP* 3.6 26.1 - - + -
57A GLN* 2.8 38.2 + - - +
156A THR 3.1 11.3 + - - +
157A ASP* 3.6 10.1 - - - +
159A PHE* 1.3 77.0 - - - +
161A ALA* 1.3 60.8 + - - +
163A ALA* 3.1 6.0 + - - +
164A ASN* 2.9 61.7 + - - +
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Residues in contact with ALA 161 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A VAL* 4.3 7.6 - - + -
113A ILE* 4.2 13.5 - - + -
120A ILE* 3.9 18.4 - - + -
157A ASP 2.9 17.4 + - - +
158A HIS* 3.1 9.4 + - - +
160A ARG* 1.3 76.8 - - - +
162A TRP* 1.3 64.5 + - + +
164A ASN* 3.5 9.3 + - - +
165A ARG* 3.0 34.4 + - - +
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Residues in contact with TRP 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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91A PHE* 3.5 41.3 - + + -
92A TYR 3.4 23.1 - - - -
93A ILE* 3.9 14.8 - - + -
120A ILE* 3.7 25.8 - - + -
140A TYR* 3.9 16.8 - + + -
141A TRP 3.6 9.8 + - - -
142A SER* 2.8 27.3 + - - -
158A HIS* 2.8 19.8 + - + +
159A PHE* 3.5 35.4 - + - +
161A ALA* 1.3 75.4 - - + +
163A ALA* 1.3 66.2 + - - +
165A ARG* 2.9 14.5 + - - +
166A GLY 3.4 0.2 + - - -
167A LEU* 3.0 41.9 + - + +
169A LEU* 4.0 12.6 - - + -
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Residues in contact with ALA 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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56A TRP* 3.8 27.6 - - + -
159A PHE 2.9 14.3 + - - +
160A ARG* 3.4 15.3 - - - +
162A TRP* 1.3 77.5 - - - +
164A ASN* 1.3 57.3 + - - +
165A ARG 3.0 5.4 + - - -
166A GLY* 3.0 15.1 + - - -
167A LEU 3.4 13.2 + - - +
168A ASN* 5.1 4.0 - - + +
169A LEU 6.1 0.2 - - - +
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Residues in contact with ASN 164 (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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160A ARG* 2.9 52.2 + - - +
161A ALA* 3.8 9.0 - - - +
162A TRP 3.2 0.4 - - - -
163A ALA* 1.3 76.0 - - - +
165A ARG* 1.3 70.0 + - - +
166A GLY 3.5 0.6 + - - -
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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