Contacts of the strand formed by residues 129 - 134 (chain D) in PDB entry 4GDK
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 129 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55D ILE* 4.3 5.4 - - + -
56D ASP 2.9 11.6 + - - +
57D ILE* 3.5 28.5 - - + +
58D LEU 3.2 19.8 + - - -
104D VAL* 4.5 9.2 - - + -
116D VAL* 3.9 25.6 - - + +
119D LEU* 3.7 35.7 - - + +
120D TYR* 4.0 13.0 - - + -
123D PHE 4.4 13.9 - - - +
124D GLY* 4.7 0.7 - - - -
128D LYS* 1.3 72.3 - - - +
130D VAL* 1.3 66.2 + - - +
131D LEU* 3.8 27.8 - - + -
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Residues in contact with VAL 130 (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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58D LEU* 3.5 21.8 - - + +
60D LYS* 4.0 21.3 - - + +
103D TYR 4.0 4.7 - - - +
104D VAL* 4.5 5.9 - - - +
105D ASN 4.7 4.3 + - - -
123D PHE 5.7 0.8 + - - -
125D SER 6.0 0.2 - - - +
128D LYS* 4.1 25.9 + - + +
129D LEU* 1.3 77.6 - - - +
131D LEU* 1.3 71.0 + - - +
132D HIS* 3.8 29.5 - - + +
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Residues in contact with LEU 131 (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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57D ILE* 4.1 19.5 - - + -
58D LEU 2.9 6.7 + - - -
59D LEU* 3.4 19.5 - - + +
60D LYS 3.0 23.4 + - - -
81D ILE* 4.3 9.9 - - + -
84D LEU* 3.8 28.3 - - + -
102D ILE* 3.9 26.0 - - + -
103D TYR 3.6 3.4 - - - +
104D VAL* 3.7 28.3 - - + -
116D VAL* 5.3 0.2 - - + -
129D LEU* 3.6 22.0 + - + -
130D VAL* 1.3 84.6 - - - +
132D HIS* 1.3 64.0 + - - +
133D TYR 4.0 0.5 + - - -
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Residues in contact with HIS 132 (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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60D LYS* 3.2 33.2 + - + +
61D ALA 4.9 1.1 + - - -
62D VAL* 3.7 26.0 - - + +
101D PHE 3.6 0.5 - - - +
102D ILE* 3.2 5.2 - - - -
103D TYR* 2.8 45.1 + - + +
105D ASN 5.9 1.1 - - - -
106D GLN* 3.2 48.3 + - + +
130D VAL* 3.8 24.8 - - + +
131D LEU* 1.3 73.0 - - - +
133D TYR* 1.3 60.2 + - - +
139D TRP* 4.3 13.2 - + + -
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Residues in contact with TYR 133 (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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59D LEU* 3.7 27.7 + - + -
60D LYS 2.9 29.3 + - - -
61D ALA* 3.4 22.8 + - + +
62D VAL* 3.0 27.0 + - - +
65D THR* 3.7 11.6 + - + -
66D PRO 3.4 20.9 - - - -
67D ILE* 3.7 3.3 - - - +
68D MET* 2.8 38.3 + - + +
71D LYS* 5.3 1.9 - - - +
88D ILE* 4.5 19.5 - - + -
92D LEU* 4.0 13.0 - - + -
100D LEU* 4.2 10.1 - - + -
101D PHE 3.2 8.1 - - - +
102D ILE* 4.6 5.8 - - + -
131D LEU 4.5 1.1 - - - -
132D HIS* 1.3 75.0 - - - +
134D CYS* 1.3 62.6 + - - +
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Residues in contact with CYS 134 (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* 3.2 29.2 - - + +
63D GLY 3.9 7.9 - - - -
65D THR* 3.4 8.1 - - - -
100D LEU* 3.4 9.7 - - - +
101D PHE* 2.6 40.6 + - - +
103D TYR* 4.7 4.9 - - + -
133D TYR* 1.3 78.9 - - - +
135D LYS* 1.3 62.2 + - - +
136D SER* 3.1 41.0 + - - +
138D ALA* 4.3 14.6 - - + -
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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