Contacts of the helix formed by residues 113 - 121 (chain B) in PDB entry 4FZY
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 SER 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B HIS* 3.4 0.4 - - - -
111B LYS* 3.8 1.2 - - - +
112B TYR* 1.3 82.2 - - - +
114B ASN* 1.3 67.4 + - - +
115B MET* 3.1 5.6 + - - +
116B ALA* 2.9 30.9 + - - +
117B LEU* 3.2 18.9 + - - +
10D A 3.5 19.3 + - - -
11D C 3.9 15.7 - - - -
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Residues in contact with ASN 114 (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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80B HIS* 3.2 25.7 + - + -
113B SER* 1.3 72.5 - - - +
115B MET* 1.3 64.6 + - + +
117B LEU* 3.7 3.8 + - - +
118B TYR* 3.4 17.8 + - - +
139B ASP* 3.6 32.9 + - - +
142B ILE* 3.9 14.6 - - - +
143B THR* 2.6 36.4 + - - -
146B LEU* 4.6 6.1 - - - +
11D C 3.0 20.0 + - - +
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Residues in contact with MET 115 (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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113B SER* 3.1 4.8 + - - +
114B ASN* 1.3 80.6 - - + +
116B ALA* 1.3 64.4 + - - +
117B LEU 3.4 0.2 - - - -
118B TYR* 3.4 25.1 - - - +
119B LYS* 3.3 23.5 + - - +
133B HIS* 4.5 23.8 - - + +
138B TYR* 4.5 12.3 - - + -
139B ASP* 4.6 5.6 - - - +
142B ILE* 4.1 28.5 - - + -
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Residues in contact with ALA 116 (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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111B LYS* 4.0 28.9 - - + +
113B SER* 2.9 23.6 + - - +
115B MET* 1.3 77.1 - - - +
117B LEU* 1.3 60.3 + - - +
119B LYS* 3.4 12.1 + - + +
120B THR* 2.9 35.5 + - - +
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Residues in contact with LEU 117 (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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80B HIS* 3.6 17.0 - - + -
103B ALA* 3.9 24.5 - - + -
107B TRP* 5.1 5.4 - - + -
110B ILE* 3.7 22.0 - - + -
111B LYS 3.0 23.3 - - - +
112B TYR* 3.5 26.5 - - + +
113B SER 3.2 22.3 + - - +
114B ASN 3.9 4.0 - - - +
116B ALA* 1.3 74.4 - - - +
118B TYR* 1.3 65.4 + - - +
120B THR* 4.4 2.2 - - - -
121B ARG* 2.9 32.8 + - + +
123B LEU* 4.6 0.2 - - - +
146B LEU* 4.0 21.5 - - + -
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Residues in contact with TYR 118 (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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114B ASN 3.4 11.1 + - - +
115B MET* 3.4 26.5 - - - +
116B ALA 3.2 0.4 - - - -
117B LEU* 1.3 80.3 - - - +
119B LYS* 1.3 61.3 + - + +
121B ARG 3.7 0.7 - - - -
122B LYS 3.0 5.9 + - - -
123B LEU* 3.0 73.5 + - + +
124B ASN* 3.3 7.4 + - - -
125B VAL* 3.0 40.1 + - + +
127B THR* 5.4 0.9 - - - +
138B TYR* 5.9 1.1 - - - -
142B ILE* 3.8 42.0 - - + +
145B ALA* 4.3 4.0 - - + -
146B LEU* 5.3 2.0 - - + +
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Residues in contact with LYS 119 (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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115B MET* 3.3 12.9 + - - +
116B ALA* 3.5 14.7 - - - +
118B TYR* 1.3 82.9 - - + +
120B THR* 1.3 66.9 + - - +
122B LYS* 2.8 30.3 + - - +
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Residues in contact with THR 120 (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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110B ILE* 4.1 31.7 - - + +
111B LYS* 5.3 3.5 + - - +
116B ALA* 2.9 19.6 + - - +
117B LEU* 4.0 5.4 - - - -
119B LYS* 1.3 87.8 - - - +
121B ARG* 1.3 68.1 + - - +
122B LYS* 3.5 14.2 + - - +
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Residues in contact with ARG 121 (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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107B TRP* 3.3 59.5 - - + +
110B ILE* 5.8 0.9 - - - -
117B LEU* 2.9 27.1 + - + +
120B THR* 1.3 85.2 + - + +
122B LYS* 1.3 74.3 + - - +
123B LEU* 3.3 18.4 + - + +
146B LEU* 4.7 5.2 - - + -
149B ASP* 2.7 38.9 + - - +
153B THR* 4.2 6.1 + - - +
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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