Contacts of the strand formed by residues 105 - 112 (chain A) in PDB entry 3ZTX
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 GLY 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A LYS 4.7 0.2 - - - -
102A GLY* 3.0 31.7 + - - +
104A PHE* 1.3 80.7 + - - -
106A ASN* 1.3 75.3 + - - +
107A VAL* 6.0 0.2 - - - -
122A LYS* 5.5 6.7 - - - -
123A VAL 3.4 11.1 + - - -
124A LEU* 4.2 6.5 - - - +
125A PHE* 5.0 1.4 - - - -
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Residues in contact with ASN 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A GLY 3.6 5.5 - - - +
101A LYS* 3.4 28.8 + - - +
102A GLY 5.1 1.0 + - - -
105A GLY* 1.3 89.8 + - - +
107A VAL* 1.3 61.3 + - - +
108A TYR* 3.5 31.4 + - + +
121A LEU 3.7 1.7 - - - +
122A LYS* 3.5 2.5 - - - +
123A VAL* 2.8 41.9 + - + +
125A PHE* 4.9 14.1 - - - -
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A PRO* 3.7 4.0 - - - +
99A LEU* 2.7 33.2 + - + -
100A GLY 2.9 14.5 + - - +
105A GLY 6.0 0.2 - - - -
106A ASN* 1.3 75.7 - - - +
108A TYR* 1.3 62.3 + - - +
120A ALA* 3.7 27.8 - - + -
121A LEU 3.4 9.4 - - - +
122A LYS* 4.0 27.1 - - + +
1357A ZTX 3.7 51.4 - - + +
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Residues in contact with TYR 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ILE* 4.0 32.8 - - + -
97A ARG 3.4 5.8 - - - +
98A PRO* 3.8 31.6 - - + -
99A LEU* 3.9 4.9 - - - -
106A ASN* 3.5 40.9 + - + +
107A VAL* 1.3 74.3 - - - +
109A LEU* 1.3 68.1 + - - +
110A ALA* 3.4 0.3 + - - +
120A ALA* 3.2 4.9 - - - -
121A LEU* 2.9 42.1 + - + +
123A VAL* 3.9 19.7 - - + -
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ILE* 3.8 1.6 - - - -
96A GLY* 2.7 31.2 + - - -
97A ARG* 2.9 44.7 + - + +
99A LEU* 3.5 15.0 - - + +
108A TYR* 1.3 74.6 - - - +
110A ALA* 1.3 55.4 + - - +
118A ILE* 3.6 26.7 - - + -
119A MET 3.6 9.6 - - - +
172A PHE* 3.8 29.6 - - + -
801D TRP* 4.0 21.3 - - + -
802D ALA* 4.1 3.6 - - + -
807D LEU* 3.9 23.1 - - + -
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A PHE* 4.5 9.0 - - + -
94A ASP 3.4 10.5 - - - +
95A ILE* 4.2 6.1 - - + -
108A TYR 4.2 3.8 - - - +
109A LEU* 1.3 76.8 - - - +
111A ARG* 1.3 58.7 + - - +
112A GLU 4.2 0.4 - - - -
117A PHE 3.8 0.2 - - - +
118A ILE* 3.4 4.3 - - - +
119A MET* 2.7 45.7 + - + +
121A LEU* 3.9 34.8 - - + +
801D TRP* 3.9 4.3 - - - -
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Residues in contact with ARG 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A PHE* 3.3 3.8 - - - -
94A ASP* 2.9 61.7 + - - +
110A ALA* 1.3 73.1 - - - +
112A GLU* 1.3 65.9 + - - +
113A LYS* 3.2 2.9 + - - +
116A LYS* 3.6 66.8 - - - +
117A PHE 3.4 3.6 - - - +
118A ILE* 4.1 12.3 - - + -
801D TRP* 3.4 61.1 - - + +
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A PHE* 4.0 13.3 - - + -
92A ASP* 3.5 11.9 - - - +
93A PHE* 3.5 28.5 - - + -
110A ALA 4.2 0.4 - - - -
111A ARG* 1.3 70.8 - - - +
113A LYS* 1.3 60.1 + - - +
114A GLN* 3.0 32.9 + - - +
115A ASN* 3.0 24.9 + - - +
116A LYS* 2.9 30.1 + - - -
117A PHE 2.9 12.9 + - - +
119A MET* 4.2 4.4 - - + +
825D TYR* 2.7 45.7 + - + +
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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