Contacts of the strand formed by residues 105 - 111 (chain D) in PDB entry 4QZU
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D TYR* 5.1 2.3 + - - -
95D CYS 3.1 14.8 - - - -
97D GLN* 3.9 14.1 - - - +
104D ARG* 1.3 80.3 - - - +
106D TRP* 1.3 68.6 + - - +
119D LEU* 3.8 2.3 - - - +
120D THR* 3.0 34.4 + - - +
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Residues in contact with TRP 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D VAL* 5.4 7.1 - - + +
64D PHE* 4.0 24.2 - + - -
86D VAL* 4.1 6.1 - - + -
93D LEU* 3.8 45.3 - - + -
94D VAL* 4.1 0.3 - - - +
95D CYS* 2.8 66.7 + - + +
97D GLN* 4.7 11.8 - - - +
105D GLY* 1.3 79.2 - - - +
107D LYS* 1.3 70.4 + - - +
108D GLN* 3.9 21.8 - - + -
117D LEU* 3.9 10.5 - - + -
118D GLU 3.1 13.9 - - - +
119D LEU* 3.8 21.8 - - + -
120D THR* 4.6 1.8 - - - +
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Residues in contact with LYS 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A TYR* 2.2 45.9 + - + +
75A LYS* 3.7 13.8 - - - +
81A HIS* 5.1 0.8 + - - -
89D GLU* 4.6 4.6 + - - -
92D VAL* 3.8 11.7 - - + -
93D LEU 3.2 4.7 - - - -
94D VAL* 4.1 28.5 - - + -
106D TRP* 1.3 81.2 - - - +
108D GLN* 1.3 61.1 + - - +
109D TRP* 3.9 12.0 - - + -
116D TYR 3.8 0.3 - - - +
117D LEU* 3.4 2.8 - - - +
118D GLU* 2.8 46.1 + - + +
120D THR* 6.5 1.3 - - + -
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Residues in contact with GLN 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D GLN* 2.9 32.5 + - - +
40D LYS* 3.8 14.9 + - - +
42D ILE* 3.5 19.0 - - - +
49D PHE* 5.1 2.2 - - - -
51D THR* 5.7 2.8 - - - +
64D PHE* 6.1 0.4 - - - -
92D VAL* 4.3 0.4 - - - +
93D LEU* 2.8 41.4 + - + +
106D TRP* 3.9 19.3 - - + -
107D LYS* 1.3 76.2 - - - +
109D TRP* 1.3 65.0 + - - +
115D LEU* 3.7 26.2 - - + +
116D TYR 3.2 11.9 - - - +
117D LEU* 3.7 17.1 - - + +
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Residues in contact with TRP 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LYS* 3.5 50.5 - - + -
76A SER* 4.3 11.6 - - - -
79A ASN* 4.8 1.1 - - - -
4D GLN* 3.6 6.7 - - - +
91D ASP 3.8 7.2 - - - +
92D VAL* 4.1 9.0 - - + -
107D LYS 3.9 16.2 - - - -
108D GLN* 1.3 83.4 - - - +
110D ILE* 1.3 70.7 + - - +
111D GLU* 3.1 34.4 + - + -
115D LEU* 3.6 2.1 - - - -
116D TYR* 2.8 70.3 + + + -
117D LEU 5.4 0.4 - - - -
118D GLU* 4.2 19.1 - - + -
127D ARG* 6.5 0.2 - - + -
202D ACT 3.6 23.3 - - + -
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Residues in contact with ILE 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ASP* 4.6 2.3 - - - +
1D THR* 4.1 31.9 + - + +
3D ASP 4.1 11.2 - - - +
4D GLN* 3.9 23.3 - - + +
8D TRP* 3.6 37.0 - - + -
91D ASP 4.8 1.6 + - - -
109D TRP* 1.3 75.9 - - - +
111D GLU* 1.3 71.0 + - - +
112D GLY 3.4 21.3 - - - +
114D LYS 3.4 6.5 - - - +
115D LEU* 3.9 24.0 - - + -
202D ACT 3.9 13.3 - - - +
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Residues in contact with GLU 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ASN* 2.7 38.9 + - + +
60A TYR* 3.5 3.6 - - - -
61A ASP* 3.7 30.7 - - + +
75A LYS* 3.9 6.8 - - - +
76A SER* 3.0 15.5 + - - -
109D TRP* 3.1 13.6 + - + -
110D ILE* 1.3 75.9 - - - +
112D GLY* 1.3 63.6 + - - +
113D ASP 3.6 0.2 + - - -
114D LYS* 3.1 14.6 + - - +
116D TYR* 3.5 31.8 + - + -
202D ACT 2.9 34.6 - - - +
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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