Contacts of the strand formed by residues 201 - 206 (chain N) in PDB entry 4G7Z
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 201 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184N GLU* 4.3 10.3 - - - -
185N VAL* 2.6 42.8 + - - +
199N LEU 4.2 0.6 + - - -
200N ASP* 1.3 74.7 - - - +
202N VAL* 1.3 63.8 + - - -
395N VAL* 4.4 3.2 - - - +
396N VAL 3.3 9.2 - - - -
397N LYS* 4.3 4.7 - - - -
398N ALA 4.8 2.7 - - - -
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Residues in contact with VAL 202 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182N GLY* 3.8 20.6 - - - +
183N GLU 4.1 2.9 - - - -
184N GLU* 3.2 25.6 - - - +
201N GLY* 1.3 72.5 - - - -
203N ALA* 1.3 63.0 + - - +
204N LEU* 3.7 19.8 - - + +
394N LEU 3.7 0.7 - - - +
395N VAL* 3.6 1.2 - - - -
396N VAL* 2.8 43.0 + - + +
398N ALA* 3.3 26.5 - - + +
400N VAL* 3.8 33.9 - - + -
445N ARG* 5.2 1.3 - - - -
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Residues in contact with ALA 203 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179N VAL* 4.9 5.2 - - + -
180N LYS 4.9 3.8 - - - +
181N ASP* 5.1 1.1 - - - -
182N GLY* 2.8 28.9 + - - -
183N GLU 3.2 10.0 + - - +
185N VAL* 3.6 26.2 - - + -
191N LEU* 4.4 7.2 - - + -
201N GLY 3.7 0.4 + - - -
202N VAL* 1.3 72.3 - - - +
204N LEU* 1.3 65.6 + - - +
393N ILE* 4.1 17.9 - - + -
394N LEU 3.6 4.9 - - - +
395N VAL* 4.4 5.2 - - + +
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Residues in contact with LEU 204 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181N ASP* 3.4 6.3 - - - +
182N GLY* 5.0 2.7 - - - +
202N VAL* 3.7 29.6 - - + +
203N ALA* 1.3 82.4 - - - +
205N TYR* 1.3 67.6 + - - +
206N ARG* 5.5 1.6 - - - -
393N ILE* 3.3 9.9 - - - +
394N LEU* 3.0 43.6 + - + +
396N VAL* 4.1 14.8 - - + -
441N ARG* 3.3 39.3 - - - +
445N ARG* 3.4 31.0 - - - +
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Residues in contact with TYR 205 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177N ALA* 3.7 29.3 + - + +
179N VAL* 3.1 23.0 + - + -
180N LYS* 3.8 7.8 - - + +
181N ASP* 2.6 43.9 + - + +
204N LEU* 1.3 77.3 - - - +
206N ARG* 1.3 70.0 + - - +
207N PHE 3.9 2.0 + - - -
208N PRO* 4.5 14.6 - - + +
357N GLU* 4.6 2.9 - - - -
387N LEU* 3.6 40.3 + - + -
388N HIS* 4.3 8.3 + - - -
390N PRO* 3.8 24.2 - - + -
392N SER 4.4 0.2 - - - -
393N ILE* 4.5 9.9 - - + -
441N ARG* 3.5 14.8 + - - +
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Residues in contact with ARG 206 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168N THR* 5.0 4.1 + - + +
204N LEU* 4.9 2.7 - - - -
205N TYR* 1.3 79.4 + - - +
207N PHE* 1.3 80.4 + - + +
208N PRO 3.8 0.2 - - - -
390N PRO* 3.7 1.1 - - - +
391N ALA* 2.8 32.9 + - - +
392N SER* 3.1 35.2 + - - +
394N LEU* 3.8 41.1 - - + +
98P GLU* 4.7 7.1 - - - +
101P GLU* 2.7 39.1 + - - -
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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
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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