Contacts of the strand formed by residues 105 - 113 (chain C) in PDB entry 4TZQ
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 LEU 105 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C ILE* 4.6 1.1 - - + -
96C ALA* 3.3 24.7 - - + +
99C ALA* 3.8 17.2 + - + -
100C THR* 3.7 16.4 - - + -
103C GLY 3.5 0.6 - - - -
104C PHE* 1.3 77.3 - - - +
106C LYS* 1.3 61.2 + - - +
107C GLU 3.3 29.4 - - - +
108C VAL* 4.1 11.9 - - + +
129C PHE* 3.5 32.6 - - + +
131C TYR* 2.4 34.9 + - - +
199C LEU* 4.3 8.5 - - + -
200C GLU 3.9 4.9 - - - +
202C THR* 3.7 2.7 - - - -
211C ILE* 4.8 9.9 - - + -
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Residues in contact with LYS 106 (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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105C LEU* 1.3 72.6 - - - +
107C GLU* 1.3 63.5 + - + +
128C LYS* 3.5 2.6 - - - +
129C PHE* 2.8 33.2 + - - +
142C SER* 3.4 11.0 - - - +
143C THR 4.3 11.0 + - - -
144C ASP* 5.4 0.2 + - - -
145C LYS* 4.1 10.4 - - - +
150C ASP* 3.3 37.7 + - - +
152C HIS* 4.1 13.5 + - + +
200C GLU* 2.9 49.5 + - + +
201C TYR 4.0 15.7 - - - +
202C THR* 3.7 19.2 - - + +
203C ASN* 5.2 3.8 - - - -
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Residues in contact with GLU 107 (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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105C LEU* 3.3 7.6 - - - +
106C LYS* 1.3 85.8 - - + +
108C VAL* 1.3 63.3 + - - +
109C SER* 2.6 24.2 + - - +
126C SER* 3.6 2.7 - - - -
127C MET 3.3 13.7 - - - +
128C LYS* 3.4 30.0 - - + +
129C PHE* 4.3 0.9 - - - -
199C LEU* 3.1 7.7 - - - +
200C GLU* 2.9 33.6 + - + +
220C PHE* 3.8 24.5 - - + -
221C TYR* 2.7 27.9 + - - -
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Residues in contact with VAL 108 (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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46C ILE* 4.6 9.6 - - + -
50C PHE* 3.6 23.0 - - + -
93C LEU* 4.8 5.8 - - + -
96C ALA* 4.3 17.9 - - + -
105C LEU* 4.1 13.7 - - + +
107C GLU* 1.3 73.4 - - - +
109C SER* 1.3 63.5 + - - +
127C MET* 3.0 25.0 + - + -
129C PHE* 3.8 24.0 - - + -
197C PHE* 4.4 17.9 - - + -
198C ARG 3.6 6.5 - - - +
199C LEU* 4.3 7.4 - - + -
214C PHE* 4.9 7.0 - - + -
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Residues in contact with SER 109 (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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50C PHE* 4.3 1.1 - - - -
107C GLU* 2.6 28.7 + - - +
108C VAL* 1.3 81.6 + - - +
110C LEU* 1.3 61.8 + - - +
111C VAL* 3.5 13.6 + - - +
124C VAL* 4.3 6.1 - - - -
125C PHE 3.3 11.7 - - - -
126C SER* 3.2 12.9 - - - -
197C PHE* 3.4 7.2 - - - -
198C ARG 2.9 40.9 + - - -
221C TYR* 4.3 4.0 - - - -
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Residues in contact with LEU 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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50C PHE* 3.8 13.3 - - + -
53C VAL* 4.0 20.6 - - + -
54C LEU* 3.8 19.1 - - + -
59C ILE* 3.8 26.9 - - + -
109C SER* 1.3 70.0 - - - +
111C VAL* 1.3 60.0 + - - +
112C ILE* 4.9 4.4 - - + +
123C GLU 4.0 0.7 - - - +
124C VAL* 3.5 5.0 - - - +
125C PHE* 3.0 37.1 + - + +
195C ALA* 4.1 22.0 - - + -
196C ASN 3.6 15.9 - - - +
197C PHE* 3.7 32.5 - - + -
496D ILE* 5.4 1.6 - - + -
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Residues in contact with VAL 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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109C SER* 3.6 17.0 - - - +
110C LEU* 1.3 75.6 - - - +
112C ILE* 1.3 62.5 + - - +
113C THR* 3.9 4.5 + - + +
119C LEU 5.5 0.2 - - - +
121C ALA* 3.7 24.2 - - + -
123C GLU 4.0 1.8 - - - -
124C VAL* 4.3 3.4 - - + -
194C THR 3.6 2.3 - - - +
195C ALA* 3.4 3.7 - - - -
196C ASN* 2.8 35.8 + - - +
198C ARG* 3.5 53.6 - - + +
221C TYR* 4.0 22.7 - - + -
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Residues in contact with ILE 112 (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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59C ILE* 3.9 23.1 - - + -
110C LEU* 4.9 5.6 - - + +
111C VAL* 1.3 75.8 - - - +
113C THR* 1.3 64.3 - - - +
121C ALA* 3.4 4.2 - - - -
122C ILE* 2.7 44.3 + - + -
123C GLU* 2.8 48.3 + - + +
125C PHE* 4.8 6.1 - - + -
189C LEU* 3.8 26.9 - - + -
193C PHE* 4.2 15.3 - - + -
194C THR 3.5 3.6 - - - +
195C ALA* 4.2 15.0 - - + -
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Residues in contact with THR 113 (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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111C VAL* 4.1 5.8 - - + +
112C ILE* 1.3 79.1 - - - +
114C ASN* 1.3 59.1 + - - +
115C ASN 2.6 27.3 + - - -
116C GLU* 4.5 0.9 - - - -
117C GLY 4.7 0.2 + - - -
118C ASP* 3.7 18.4 - - - +
120C GLU 4.0 3.8 - - - +
121C ALA* 4.0 14.8 - - - -
122C ILE* 3.8 10.8 - - - +
193C PHE* 3.4 9.4 - - - +
194C THR* 2.9 37.7 + - - +
198C ARG* 3.6 28.2 + - - +
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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
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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