Contacts of the strand formed by residues 237 - 241 (chain B) in PDB entry 6ZGI
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 ARG 237 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B VAL* 4.0 27.5 - - + +
84B LEU 3.4 14.4 - - - +
85B PRO* 4.8 3.6 - - + -
86B PHE* 4.2 3.4 - - - +
106B PHE* 3.6 1.2 - - - -
107B GLY 2.9 30.4 + - - +
108B THR 3.3 22.4 + - - +
109B THR* 3.8 17.2 + - - +
110B LEU* 4.0 17.5 - - + +
235B ILE* 4.0 3.3 - - - +
236B THR* 1.3 92.4 - - + +
238B PHE* 1.3 67.3 + - - +
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Residues in contact with PHE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B VAL* 3.6 3.7 - - - +
84B LEU* 2.9 66.7 + - + +
85B PRO 3.1 29.2 - - - -
86B PHE* 4.1 11.4 - + + -
90B VAL* 3.8 31.9 - - + -
92B PHE* 4.8 7.4 - + - -
104B TRP* 4.4 15.0 - + - -
105B ILE 3.1 13.2 - - - +
106B PHE* 3.5 28.7 - + + -
110B LEU* 5.7 2.7 - - - +
194B PHE* 6.2 1.6 - + - -
237B ARG* 1.3 76.5 - - - +
239B GLN* 1.3 67.3 + - - +
240B THR* 4.4 11.4 - - - -
267B VAL* 4.3 8.7 - - + -
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Residues in contact with GLN 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ASN* 3.1 21.9 - - - +
82B PRO 4.0 11.0 - - - +
83B VAL* 3.2 28.2 + - + +
84B LEU* 6.2 0.2 - - - -
104B TRP* 3.4 2.4 - - - -
105B ILE* 2.9 60.3 + - + +
110B LEU* 5.2 5.6 - - + +
135B PHE* 6.0 0.2 - - - +
136B CYS 4.8 2.8 + - - -
137B ASN 4.5 7.8 + - - +
139B PRO* 3.7 28.0 - - + +
238B PHE* 1.3 81.2 - - - +
240B THR* 1.3 73.6 + - - +
241B LEU* 3.7 0.8 - - + +
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Residues in contact with THR 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ASN* 4.0 18.2 + - - +
82B PRO 4.6 3.3 + - - -
84B LEU* 5.2 2.6 - - - +
92B PHE* 3.9 26.0 - - + -
101B ILE* 4.0 22.9 - - + -
103B GLY 3.6 12.3 - - - +
104B TRP* 3.9 6.9 - - + -
139B PRO* 5.0 4.0 - - - +
238B PHE* 4.4 7.3 - - - -
239B GLN* 1.3 84.9 - - - +
241B LEU* 1.3 65.5 + - - +
242B LEU* 4.0 17.9 + - + +
265B TYR* 4.0 22.8 + - + -
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Residues in contact with LEU 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ILE* 3.7 1.2 - - - -
102B ARG* 2.6 34.2 + - - -
103B GLY 2.9 20.2 + - - +
104B TRP 4.1 5.4 - - - +
105B ILE* 3.7 32.8 - - + +
118B LEU* 4.1 18.2 - - + -
120B VAL* 4.0 26.7 - - + -
139B PRO* 4.6 23.3 - - + +
140B PHE* 5.7 0.2 - - - +
141B LEU* 4.3 11.0 - - + -
159B VAL* 4.1 16.6 - - + -
239B GLN* 3.7 12.6 - - + +
240B THR* 1.3 74.7 - - - +
242B LEU* 1.3 55.9 + - - +
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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