Contacts of the strand formed by residues 165 - 172 (chain I) in PDB entry 6NZD
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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48I ARG* 5.1 10.1 + - - +
137I MET* 6.1 0.9 - - - +
138I LEU* 5.0 4.9 - - - +
159I TYR* 3.3 11.1 - - - -
160I ILE* 2.9 54.3 + - + +
163I PRO* 3.7 31.2 - - + +
164I PRO* 1.3 77.8 - - - +
166I LEU* 1.3 60.0 + - - +
316I ILE* 3.9 19.7 - - + +
317I PHE 3.4 5.2 - - - +
318I SER* 3.4 29.6 + - - +
319I LEU* 4.6 2.8 - - - +
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Residues in contact with LEU 166 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186H TRP* 5.7 1.3 - - + +
157I ILE* 4.7 4.7 - - + -
158I HIS 3.6 10.1 - - - +
159I TYR* 4.3 18.6 - - + -
165I GLN* 1.3 74.5 - - - +
167I MET* 1.3 84.2 + - - +
168I ILE* 4.5 0.4 - - + -
316I ILE* 3.3 5.4 - - - +
317I PHE* 2.9 53.4 + - + +
319I LEU* 4.6 14.1 - - + +
329I PHE* 5.6 3.6 - - + -
330I GLN* 5.1 9.9 - - + +
333I PHE* 3.6 30.3 - - + -
334I PHE* 3.8 28.7 - - + -
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Residues in contact with MET 167 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138I LEU* 3.8 28.3 - - + +
141I MET* 3.7 25.6 - - + -
142I MET* 4.7 8.7 - - + -
157I ILE* 3.4 6.6 - - - +
158I HIS* 2.9 57.4 + - + +
160I ILE* 3.8 11.2 - - + -
166I LEU* 1.3 80.8 - - - +
168I ILE* 1.3 63.6 + - - +
169I SER* 3.5 23.6 - - - +
314I SER* 3.8 15.0 - - - +
315I ILE 3.0 12.6 - - - +
316I ILE* 3.7 12.1 - - + -
317I PHE* 5.2 0.2 - - - -
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Residues in contact with ILE 168 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155I LEU* 4.2 24.2 - - + -
156I LYS 3.4 10.3 - - - +
157I ILE* 4.4 4.5 - - + +
166I LEU* 4.5 1.3 - - + -
167I MET* 1.3 75.2 - - - +
169I SER* 1.3 68.6 + - - +
313I ILE 3.9 0.4 - - - +
314I SER* 3.1 5.5 + - - -
315I ILE* 2.9 37.4 + - + +
317I PHE* 3.8 17.3 - - + -
333I PHE* 3.6 37.0 - - + -
339I LEU* 3.7 17.7 - - + -
340I PHE* 6.2 1.1 - - + -
343I HIS* 4.2 27.1 - - + +
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Residues in contact with SER 169 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142I MET* 3.7 31.4 - - - +
154I THR 4.2 0.4 - - - -
155I LEU* 3.2 8.7 - - - +
156I LYS* 2.9 44.2 + - - -
158I HIS* 3.7 8.3 - - - -
167I MET* 3.5 22.9 - - - +
168I ILE* 1.3 79.9 + - - +
170I LYS* 1.3 61.7 + - - +
171I VAL* 5.2 2.0 - - - -
313I ILE 3.3 5.6 - - - -
314I SER* 4.3 0.2 - - - -
343I HIS* 4.9 0.4 - - - -
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Residues in contact with LYS 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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179H ARG* 5.4 1.2 - - - +
153I SER* 4.9 12.4 - - - -
154I THR 3.2 10.1 + - - +
155I LEU* 3.5 45.6 - - - +
169I SER* 1.3 73.7 - - - +
171I VAL* 1.3 65.4 + - - +
172I PHE* 4.0 13.9 - - + -
311I ILE 4.0 1.2 - - - +
312I ALA* 3.3 2.3 - - - -
313I ILE* 2.9 33.9 + - - +
340I PHE* 4.1 4.9 - - - -
343I HIS* 3.9 16.8 - - + -
344I MET* 3.8 30.6 - - + -
347I LEU* 3.7 30.1 - - + -
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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
----------------------------------------------------------
142I MET* 3.6 25.6 - - + +
143I PHE* 5.2 0.9 - - + -
148I MET* 4.0 20.9 - - + -
152I GLY 4.1 0.3 - - - +
153I SER* 3.4 4.9 - - - -
154I THR* 2.9 35.3 + - - +
156I LYS* 3.7 15.5 - - - +
169I SER* 5.2 2.7 - - - -
170I LYS* 1.3 79.4 - - - +
172I PHE* 1.3 66.6 + - - +
310I LYS* 3.8 31.0 - - + -
311I ILE 3.7 7.2 - - - +
312I ALA* 3.8 14.6 - - + +
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Residues in contact with PHE 172 (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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151I LYS* 6.0 1.6 - - - +
152I GLY 3.6 17.0 - - - +
153I SER* 4.3 8.1 - - - +
170I LYS* 4.0 17.7 - - + -
171I VAL* 1.3 79.5 - - - +
173I SER* 1.3 58.8 + - - +
174I ALA 3.7 16.8 - - - +
310I LYS* 3.3 9.5 - - - +
311I ILE* 2.9 61.1 + - + -
313I ILE* 4.0 15.7 - - + -
347I LEU* 3.6 34.8 - - + -
351I ILE* 3.6 30.1 - - + -
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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
------------------------------------------------------------
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