Contacts of the strand formed by residues 170 - 174 (chain A) in PDB entry 1JD7
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 GLY 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A ILE 3.1 5.1 + - - -
82A TYR* 3.2 23.1 - - - -
83A VAL 3.0 20.3 + - - -
168A VAL* 3.2 7.6 - - - +
169A LYS* 1.3 81.6 - - - +
171A PHE* 1.3 72.0 + - - -
196A VAL 3.1 12.1 - - - -
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Residues in contact with PHE 171 (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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82A TYR* 4.5 1.2 - - - +
83A VAL* 3.4 11.0 - - + +
85A THR* 3.7 21.5 - - - +
160A ILE* 3.4 43.1 - - + -
163A LEU* 3.6 24.9 - - + -
164A GLN* 3.5 24.0 - - + -
168A VAL* 3.6 24.5 - - + -
170A GLY* 1.3 84.2 - - - -
172A ARG* 1.3 60.7 + - - +
173A PHE* 4.2 15.7 - + + -
195A PRO* 4.0 20.9 - - + -
196A VAL 2.8 10.9 + - - +
197A VAL* 3.3 11.5 - - + +
198A PHE* 3.1 29.6 + - - +
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Residues in contact with ARG 172 (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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33A GLN* 3.6 30.5 - - + +
50A TYR* 4.2 2.0 - - - -
82A TYR* 5.7 0.2 - - + -
83A VAL 2.9 7.0 + - - +
84A ASP* 2.7 47.3 + - - +
85A THR* 2.7 33.3 + - - +
171A PHE* 1.3 72.7 - - - +
173A PHE* 1.3 63.9 + - - +
174A ASP* 2.9 26.2 + - - +
198A PHE* 3.4 33.3 - - + +
200A GLU* 3.2 40.8 + - + +
221A THR* 5.4 0.2 - - - +
263A HIS* 4.9 7.4 - - - -
264A ASP* 4.6 7.5 + - - -
900A CL 3.2 29.7 - - - +
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Residues in contact with PHE 173 (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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85A THR* 3.8 5.8 - - - -
87A ILE* 3.8 29.8 - - + -
160A ILE* 3.9 28.3 - - + -
171A PHE* 4.2 13.0 - + + -
172A ARG* 1.3 75.3 - - - +
174A ASP* 1.3 61.8 + - - +
176A SER* 2.7 30.4 + - - +
184A ILE* 4.0 18.4 - - + -
187A LEU* 4.2 11.4 - - + -
188A MET* 3.8 27.8 - - - -
197A VAL* 3.8 23.6 - - + -
198A PHE 2.9 9.5 + - - -
199A GLN* 3.9 20.6 - - + -
200A GLU 3.0 19.2 + - - -
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Residues in contact with ASP 174 (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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50A TYR* 3.3 18.3 - - - -
84A ASP* 3.7 4.0 - - - +
85A THR 2.9 20.3 + - - +
86A LEU* 3.3 30.0 - - + +
87A ILE* 3.7 17.7 + - - +
88A ASN* 4.2 1.7 - - - +
89A HIS* 3.7 8.7 - - - -
139A LEU* 5.8 0.2 - - - +
172A ARG* 2.9 33.8 + - - +
173A PHE* 1.3 71.8 - - - +
175A ALA* 1.3 84.7 + - - +
176A SER 3.2 0.9 + - - -
200A GLU* 3.7 6.5 - - - +
264A ASP* 5.8 0.3 - - - +
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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