Contacts of the strand formed by residues 105 - 111 (chain C) in PDB entry 4NZD
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 PHE 105 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C PRO 4.0 8.5 - - - +
104C PRO* 1.3 76.7 - - - +
106C ASP* 1.3 90.0 + - - +
107C VAL* 3.4 3.5 + - - -
119C TRP* 3.9 1.7 - - - +
120C ARG* 3.0 52.3 + - + +
121C SER* 3.9 22.0 - - - -
122C ASP* 3.0 28.9 - - - -
199C SER* 4.6 5.2 - - - -
200C ASP 5.8 1.1 - - - +
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Residues in contact with ASP 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C PHE* 1.3 101.3 - - - +
107C VAL* 1.3 63.7 + - - +
108C THR* 3.5 12.8 + - + +
118C SER 3.9 0.5 - - - +
119C TRP* 3.8 9.4 - - - -
120C ARG* 3.7 21.0 + - + +
200C ASP 5.9 0.4 + - - -
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Residues in contact with VAL 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C PHE* 4.4 3.8 - - - +
106C ASP* 1.3 72.0 - - - +
108C THR* 1.3 65.8 + - - +
117C ILE* 4.3 6.5 - - + -
118C SER 3.5 9.9 - - - +
119C TRP* 4.3 9.2 - - + -
179C LEU* 3.7 21.8 - - + +
180C GLN* 5.1 0.7 - - - -
181C VAL* 3.9 18.4 - - + +
199C SER* 3.4 32.3 - - - +
200C ASP 4.3 7.7 + - - +
202C VAL* 3.6 44.6 - - + +
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Residues in contact with THR 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C ASP* 4.0 10.7 + - + +
107C VAL* 1.3 80.1 - - - +
109C VAL* 1.3 65.9 + - - +
110C THR* 5.5 6.5 - - - -
116C GLN 3.6 0.8 - - - +
117C ILE* 3.4 6.4 - - - +
118C SER* 2.8 49.5 + - - +
202C VAL* 4.9 1.1 - - - -
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Residues in contact with VAL 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C THR* 1.3 81.9 - - - +
110C THR* 1.3 66.7 + - - +
115C TYR* 5.9 5.8 - - + -
116C GLN 3.3 2.2 - - - +
117C ILE* 3.6 29.6 - - + -
171C PHE* 6.4 0.2 - - + -
179C LEU* 4.9 8.5 - - + -
202C VAL* 4.4 17.3 - - + -
204C PHE* 3.4 58.5 - - + +
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Residues in contact with THR 110 (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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127A ALA* 5.2 17.0 - - + +
108C THR* 5.5 6.3 - - - -
109C VAL* 1.3 81.2 - - - +
111C PHE* 1.3 61.3 + - - +
112C SER* 6.0 0.3 - - - -
115C TYR* 3.6 5.2 - - - +
116C GLN* 2.7 56.5 + - - +
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Residues in contact with PHE 111 (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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110C THR* 1.3 76.5 - - - +
112C SER* 1.3 62.0 + - - +
113C GLY* 3.4 39.0 - - - -
114C GLN* 3.3 14.1 - - - -
115C TYR* 3.7 33.7 - + + -
168C PRO* 4.5 7.9 - - + -
207C GLN* 3.4 53.2 - - + +
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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