Contacts of the strand formed by residues 237 - 241 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C VAL* 4.0 29.0 - - + +
84C LEU 3.4 13.9 - - - +
85C PRO* 4.8 3.8 - - + -
86C PHE* 4.2 3.1 - - - +
106C PHE* 3.6 1.0 - - - -
107C GLY 2.9 30.3 + - - +
108C THR 3.3 22.0 + - - +
109C THR* 3.8 17.4 + - - +
110C LEU* 4.0 17.9 - - + +
235C ILE* 4.0 3.1 - - - +
236C THR* 1.3 93.0 - - + +
238C PHE* 1.3 67.2 + - - +
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Residues in contact with PHE 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C PRO 4.2 0.2 - - - +
83C VAL* 3.6 3.4 - - - -
84C LEU* 2.9 66.5 + - + +
85C PRO 3.1 28.3 - - - -
86C PHE* 4.1 10.5 - + + -
90C VAL* 3.8 31.6 - - + -
92C PHE* 4.8 7.9 - + - -
104C TRP* 4.4 15.3 - + - -
105C ILE 3.1 13.5 - - - +
106C PHE* 3.5 29.2 - + + -
110C LEU* 5.8 2.5 - - - -
194C PHE* 6.2 2.0 - + - -
237C ARG* 1.3 76.9 - - - +
239C GLN* 1.3 67.1 + - - +
240C THR* 4.4 11.0 - - - -
267C VAL* 4.3 7.9 - - + -
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Residues in contact with GLN 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ASN* 3.1 21.5 - - + +
82C PRO 4.0 11.2 - - - +
83C VAL* 3.2 29.5 + - + +
84C LEU* 5.9 0.4 - - - -
104C TRP* 3.4 2.4 - - - -
105C ILE* 2.9 61.3 + - + +
110C LEU* 5.2 5.4 - - + +
135C PHE* 6.0 0.2 - - - +
136C CYS 4.8 2.8 + - - -
137C ASN 4.5 8.5 + - - +
139C PRO* 3.7 27.0 - - + +
238C PHE* 1.3 82.6 - - - +
240C THR* 1.3 73.4 + - - +
241C LEU* 3.7 0.7 - - + +
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Residues in contact with THR 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C ASN* 4.0 18.5 + - - +
82C PRO 4.6 3.6 + - - -
84C LEU* 5.3 3.0 - - - +
92C PHE* 3.9 25.2 - - + -
101C ILE* 4.0 23.3 - - + -
103C GLY 3.6 11.2 - - - +
104C TRP* 3.9 7.0 - - + -
139C PRO* 5.0 3.5 - - - +
238C PHE* 4.4 6.9 - - - -
239C GLN* 1.3 84.9 - - - +
241C LEU* 1.3 64.1 + - - +
242C LEU* 4.0 16.6 + - + -
265C TYR* 4.0 23.3 + - + -
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Residues in contact with LEU 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ILE* 3.7 1.6 - - - -
102C ARG* 2.6 33.3 + - - -
103C GLY 2.9 20.0 + - - +
104C TRP 4.1 5.2 - - - +
105C ILE* 3.7 33.9 - - + +
118C LEU* 4.1 18.4 - - + -
120C VAL* 4.0 27.1 - - + -
139C PRO* 4.6 22.4 - - + +
141C LEU* 4.3 11.2 - - + -
159C VAL* 4.1 15.9 - - + -
239C GLN* 3.7 12.6 - - + +
240C THR* 1.3 75.0 - - - +
242C LEU* 1.3 55.6 + - - +
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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