Contacts of the strand formed by residues 311 - 320 (chain B) in PDB entry 1DGB
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 ILE 311 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B ILE* 4.2 13.7 - - + -
94B TYR* 4.1 21.5 - - + +
280B TYR* 3.1 4.3 - - - -
281B ILE* 2.7 52.3 + - + +
283B VAL* 3.8 33.0 - - + +
309B PRO* 4.0 9.6 - - + +
310B LEU* 1.3 76.0 - - - +
312B PRO* 1.3 79.1 - - + +
313B VAL 3.6 0.2 + - - -
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Residues in contact with PRO 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B THR* 5.1 0.4 - - - +
89B HIS* 3.2 51.2 - - + +
91B ILE* 4.3 1.4 - - - +
278B THR* 5.3 4.9 - - + -
279B PHE 3.8 1.1 - - - +
280B TYR* 3.4 26.2 - - + -
310B LEU 3.6 8.7 - - - +
311B ILE* 1.3 94.0 - - + +
313B VAL* 1.3 62.0 + - - +
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Residues in contact with VAL 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PHE* 4.1 8.5 - - + -
87B VAL* 3.6 4.2 - - + -
88B THR* 2.7 31.4 + - - -
89B HIS* 2.8 15.8 + - - +
91B ILE* 3.9 24.2 - - + -
100B PHE* 3.8 33.2 - - + -
278B THR* 5.8 0.2 - - - +
279B PHE* 2.9 21.3 + - + +
280B TYR 4.4 0.2 - - - -
281B ILE* 3.8 28.0 - - + +
311B ILE 3.6 11.2 - - - +
312B PRO* 1.3 78.1 - - - +
314B GLY* 1.3 51.9 + - - +
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Residues in contact with GLY 314 (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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85B PHE* 4.1 6.1 - - - -
86B GLU 3.1 13.7 - - - -
87B VAL* 4.3 0.2 - - - -
88B THR* 3.3 11.2 + - - -
278B THR* 3.6 9.0 - - - +
279B PHE* 2.7 35.5 + - - +
313B VAL* 1.3 84.4 - - - +
315B LYS* 1.3 61.7 + - - +
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Residues in contact with LYS 315 (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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84B TYR 3.9 0.3 - - - +
85B PHE* 3.1 10.7 - - - -
86B GLU* 2.9 38.8 + - + +
88B THR* 4.2 14.6 - - + -
239B ASP* 2.9 20.5 + - - +
276B SER* 5.0 4.9 + - - -
277B TRP 3.3 15.0 - - - +
278B THR* 2.7 32.6 + - - +
279B PHE* 4.4 0.7 - - - +
314B GLY* 1.3 76.8 - - - +
316B LEU* 1.3 63.0 + - - +
317B VAL* 4.2 12.7 - - + +
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B TYR 3.7 0.7 - - - -
85B PHE* 3.7 29.2 - - + -
109B ILE* 4.0 17.3 - - + -
111B VAL* 6.2 0.4 - - + -
132B PHE* 5.0 4.0 - - + -
134B VAL* 4.3 11.0 - - + -
136B PHE* 4.2 15.3 - - + -
236B TYR* 3.6 45.5 - - + -
275B PRO 3.9 0.2 - - - +
276B SER* 3.0 29.6 - - - -
277B TRP* 2.8 26.3 + - + +
279B PHE* 3.9 15.9 - - + -
315B LYS* 1.3 72.6 - - - +
317B VAL* 1.3 62.1 + - - +
318B LEU* 6.4 0.2 - - + -
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Residues in contact with VAL 317 (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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83B GLY* 2.9 4.9 - - - -
84B TYR* 2.8 82.2 + - + +
109B ILE* 3.7 3.6 - - - +
274B TYR* 4.4 13.0 - - + -
275B PRO 3.8 6.3 - - - +
276B SER* 4.3 11.7 - - - -
315B LYS* 4.6 9.2 - - + -
316B LEU* 1.3 84.1 - - - +
318B LEU* 1.3 74.0 + - - +
319B ASN* 4.4 4.9 - - + +
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Residues in contact with LEU 318 (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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81B ALA* 3.9 12.1 - - + -
82B PHE* 3.3 25.1 - - - +
109B ILE* 3.8 8.1 - - + -
111B VAL* 3.7 31.0 - - + -
113B PHE* 3.9 34.1 - - + -
132B PHE* 5.9 0.2 - - + -
265B LEU* 4.7 1.8 - - + -
269B ILE* 4.0 11.8 - - + +
274B TYR* 3.3 19.2 - - - +
275B PRO* 3.3 26.5 + - + +
277B TRP* 4.2 18.2 - - + -
316B LEU* 5.8 0.4 - - + -
317B VAL* 1.3 79.7 - - - +
319B ASN* 1.3 59.4 + - - +
320B ARG 3.6 0.9 - - - -
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Residues in contact with ASN 319 (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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82B PHE 2.8 9.9 + - - +
83B GLY* 3.1 12.8 - - - -
84B TYR* 3.8 25.5 - - - -
269B ILE* 3.6 13.6 - - - +
274B TYR* 3.6 40.0 + - + -
317B VAL* 4.5 4.3 - - + -
318B LEU* 1.3 74.1 - - - +
320B ARG* 1.3 65.7 + - - +
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Residues in contact with ARG 320 (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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81B ALA* 3.5 5.9 - - - +
82B PHE* 2.8 91.7 + - + +
83B GLY* 4.6 6.3 + - - +
269B ILE* 3.8 6.1 - - - +
318B LEU 3.6 1.4 - - - -
319B ASN* 1.3 87.5 + - - +
321B ASN* 1.3 73.5 + - - +
323B VAL* 5.9 4.7 - - + +
328B GLU* 4.7 5.9 + - - -
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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