Contacts of the strand formed by residues 106 - 114 (chain D) in PDB entry 1DGH
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 LYS 106 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84D TYR* 3.7 42.0 - - + -
85D PHE 3.3 4.0 - - - +
86D GLU* 3.6 32.9 + - + -
104D GLY 3.4 10.0 + - - +
105D LYS* 1.3 81.4 - - - +
107D THR* 1.3 62.6 + - - +
108D PRO* 4.4 0.8 - - - +
380D ARG* 3.8 14.4 + - - -
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Residues in contact with THR 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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84D TYR* 3.1 4.7 - - - -
85D PHE* 2.7 44.1 + - - -
99D VAL* 3.8 28.0 + - + +
105D LYS* 4.6 10.7 + - - +
106D LYS* 1.3 75.4 + - - +
108D PRO* 1.3 75.3 - - + +
109D ILE* 3.6 1.2 - - - +
136D PHE* 4.4 5.8 - - + -
137D TYR 3.4 30.7 - - - +
138D THR* 4.1 14.8 - - + +
139D GLU* 5.1 1.7 + - - -
380D ARG* 4.5 3.8 + - - +
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Residues in contact with PRO 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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83D GLY 3.6 10.8 - - - +
84D TYR* 4.2 1.6 - - + -
106D LYS 4.4 0.9 - - - +
107D THR* 1.3 94.0 - - + +
109D ILE* 1.3 63.2 + - - +
137D TYR* 3.0 37.3 + - + +
379D TYR* 3.3 29.4 - - + +
380D ARG* 3.8 29.2 - - + +
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Residues in contact with ILE 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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82D PHE* 3.6 8.0 - - - +
83D GLY 3.1 27.7 + - - +
84D TYR 3.5 29.8 - - - +
85D PHE* 3.8 7.4 - - + +
107D THR 3.6 9.6 - - - +
108D PRO* 1.3 80.4 - - - +
110D ALA* 1.3 61.1 + - - +
111D VAL* 3.9 22.2 - - + -
134D VAL* 4.1 5.4 - - + -
135D LYS 3.0 9.6 - - - +
136D PHE* 3.8 29.6 - - + -
137D TYR* 4.1 5.1 - - - -
316D LEU* 4.0 19.5 - - + -
317D VAL 4.1 9.4 - - - +
318D LEU* 4.2 3.8 - - + -
320D ARG* 5.2 0.3 + - - -
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Residues in contact with ALA 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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81D ALA 3.9 1.1 - - - -
82D PHE* 3.6 29.8 - - + -
109D ILE* 1.3 74.8 - - - +
111D VAL* 1.3 65.5 + - - +
134D VAL* 3.5 0.5 - - - -
135D LYS* 2.8 32.8 + - + -
137D TYR* 3.6 21.5 - - + +
332D ILE* 3.7 16.6 - - + -
334D PHE* 3.7 4.4 - - - -
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Residues in contact with VAL 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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80D GLY* 3.3 4.2 - - - -
81D ALA 2.9 33.6 + - - +
82D PHE* 5.7 1.6 - - - -
109D ILE* 3.9 16.2 - - + -
110D ALA* 1.3 81.1 - - - +
112D ARG* 1.3 66.6 + - - +
113D PHE* 3.7 21.3 - - + -
132D PHE* 3.5 28.3 - - + -
133D ALA 3.2 11.2 - - - +
134D VAL* 4.0 14.6 - - + -
316D LEU* 6.2 0.9 - - + -
318D LEU* 3.7 25.6 - - + -
332D ILE* 5.4 2.7 - - - +
334D PHE* 4.2 2.7 - - - -
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Residues in contact with ARG 112 (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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72D ARG* 3.4 38.9 - - - +
75D 3AH 3.1 21.0 + - - +
76D ALA 3.1 26.9 + - - -
78D GLY* 3.5 16.8 - - - +
79D ALA 3.2 12.3 - - - +
80D GLY* 4.8 0.9 - - - -
111D VAL* 1.3 77.2 - - - +
113D PHE* 1.3 66.1 + - - +
114D SER* 3.6 11.9 + - - -
131D GLY 3.6 3.1 - - - +
132D PHE* 3.8 0.7 - - - -
133D ALA 3.2 27.4 + - - -
325D TYR* 4.7 1.6 + - - -
329D VAL* 3.8 24.3 + - + +
330D GLU* 4.7 3.6 + - - +
332D ILE* 3.8 6.3 - - + -
334D PHE* 3.7 12.0 - - + -
2003D HEM 3.0 36.6 + - - +
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Residues in contact with PHE 113 (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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78D GLY* 3.0 4.3 - - - -
79D ALA 2.7 33.4 + - - +
81D ALA* 5.1 1.1 - - + -
111D VAL* 3.7 16.8 - - + -
112D ARG* 1.3 77.2 - - - +
114D SER* 1.3 65.7 + - - +
131D GLY 3.1 9.6 - - - +
132D PHE* 3.5 34.5 - + - -
209D HIS* 3.3 44.4 - + + +
212D MET* 3.6 19.7 - - + -
265D LEU* 3.6 33.9 - - + -
277D TRP* 3.9 13.5 - + - -
318D LEU* 3.7 22.9 - - + -
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Residues in contact with SER 114 (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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75D 3AH 3.3 27.7 - - - +
77D LYS 3.2 15.5 - - - -
78D GLY* 4.0 0.7 - - - -
112D ARG* 3.6 18.7 + - - -
113D PHE* 1.3 80.3 - - - +
115D THR* 1.3 66.7 + - - +
130D ARG* 3.1 16.4 - - - +
131D GLY* 2.9 29.9 + - - -
209D HIS* 4.3 5.4 + - - -
2003D HEM 4.4 3.8 + - - +
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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