Contacts of the strand formed by residues 165 - 170 (chain A) in PDB entry 3NY5
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 GLN 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A PHE* 3.6 5.7 - - - +
161A LEU* 2.7 31.8 + - + +
162A PRO 3.4 13.5 + - - +
163A ASN* 3.1 19.4 + - - +
164A LYS* 1.3 83.3 - - - +
166A ARG* 1.3 62.5 + - - +
188A ARG* 2.5 52.1 + - - +
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Residues in contact with ARG 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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159A VAL 3.3 11.9 - - - +
160A PHE* 4.1 31.0 - - + -
161A LEU* 4.0 6.8 - - - +
164A LYS 4.9 7.3 + - - +
165A GLN* 1.3 81.4 - - - +
167A THR* 1.3 65.5 + - - +
188A ARG* 3.6 12.8 + - - +
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Residues in contact with THR 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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158A ARG* 3.7 2.1 - - - +
159A VAL* 2.7 53.4 + - + +
161A LEU* 3.9 17.0 - - + -
166A ARG* 1.3 78.6 - - - +
168A VAL* 1.3 75.0 + - - +
169A VAL* 4.3 6.7 - - + +
181A LEU* 4.0 9.2 - - + -
184A ALA* 4.0 21.0 - - + +
188A ARG* 5.0 2.2 - - - -
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Residues in contact with VAL 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ILE* 3.5 41.7 - - + -
157A VAL 3.4 6.3 - - - +
158A ARG* 4.6 15.9 - - + -
167A THR* 1.3 85.5 + - - +
169A VAL* 1.3 69.0 + - - +
170A PRO* 4.7 0.9 - - - +
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Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ILE* 3.3 4.9 - - - +
157A VAL* 2.8 44.1 + - + +
159A VAL* 4.2 8.1 - - + -
167A THR* 4.3 7.8 + - + +
168A VAL* 1.3 82.9 - - - +
170A PRO* 1.3 71.7 - - + +
180A SER* 3.4 29.8 - - - +
181A LEU* 3.9 17.3 - - + -
184A ALA* 5.6 2.2 - - + -
214A ILE* 3.7 30.3 - - + -
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Residues in contact with PRO 170 (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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155A PRO 3.8 8.1 - - - +
156A ILE* 4.4 5.1 - - + -
168A VAL 4.7 0.9 - - - +
169A VAL* 1.3 95.7 - - + +
171A ALA* 1.3 60.7 + - - +
172A ARG* 3.2 35.1 + - + +
180A SER* 4.2 3.7 + - - -
214A ILE* 3.9 9.7 - - - +
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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