Contacts of the strand formed by residues 131 - 138 (chain C) 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 GLY 131 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75C HIS* 3.7 5.6 + - - -
112C ARG 4.1 2.0 - - - -
113C PHE* 3.2 10.4 - - - +
114C SER* 2.5 41.6 + - - -
130C ARG* 1.3 73.7 - - - +
132C PHE* 1.3 60.6 + - - +
133C ALA 4.0 1.6 - - - -
148C ASN* 3.3 13.0 - - - -
212C MET* 4.2 2.4 - - - +
1202C HEM 3.5 14.4 - - - -
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Residues in contact with PHE 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C VAL* 3.7 18.8 - - + -
112C ARG 3.9 2.2 - - - -
113C PHE* 3.5 33.7 - + - -
131C GLY* 1.3 73.3 - - - +
133C ALA* 1.3 59.9 + - - +
134C VAL* 4.2 8.5 - - + -
147C GLY 2.8 23.8 + - - +
148C ASN 4.4 8.3 - - - -
212C MET* 4.0 9.4 - - + -
213C ASN 3.9 6.7 - - - -
214C GLY* 3.7 11.4 - - - -
236C TYR* 2.8 54.8 + + + +
277C TRP* 3.5 42.8 - + - -
316C LEU* 5.1 4.0 - - + -
318C LEU* 5.7 0.7 - - + -
1202C HEM 3.8 0.6 - - - +
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Residues in contact with ALA 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C ALA 3.7 0.2 - - - +
111C VAL* 3.2 29.5 - - - +
112C ARG 3.3 13.8 + - - +
132C PHE* 1.3 75.3 - - - +
134C VAL* 1.3 61.3 + - - +
145C LEU 3.7 4.7 - - - -
146C VAL* 4.1 17.7 - - + +
334C PHE* 3.6 39.9 - - + -
1202C HEM 4.1 8.1 - - + +
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Residues in contact with VAL 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C ILE* 4.3 17.3 - - + -
110C ALA 3.5 2.0 - - - -
111C VAL* 4.4 8.3 - - + -
132C PHE* 4.0 13.7 - - + +
133C ALA* 1.3 79.4 - - - +
135C LYS* 1.3 63.7 + - - +
136C PHE* 3.5 32.4 - - + -
143C TRP 3.6 1.4 - - - +
144C ASP* 3.4 4.3 - - - +
145C LEU* 2.9 40.4 + - + +
236C TYR* 3.9 29.4 - - + +
316C LEU* 4.4 13.9 - - + -
334C PHE* 3.7 3.2 - - - -
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Residues in contact with LYS 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C PRO 3.6 0.2 - - - +
109C ILE* 3.0 26.7 - - - -
110C ALA* 2.8 19.6 + - + +
134C VAL* 1.3 72.9 - - - +
136C PHE* 1.3 62.0 + - - +
137C TYR* 3.5 38.5 + - + +
142C ASN* 4.2 20.5 + - + +
144C ASP* 3.0 36.3 + - - +
332C ILE* 4.1 14.6 - - - -
333C ALA 2.8 29.5 + - - -
334C PHE* 3.7 9.4 - - + -
338C ASN* 4.9 1.2 + - - -
371C LEU* 6.1 1.8 - - - +
375C VAL 3.8 10.1 - - - +
376C ASN* 4.2 7.5 + - - +
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Residues in contact with PHE 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C PHE* 3.6 37.5 - + + -
99C VAL* 4.2 8.3 - - + -
107C THR* 4.2 3.4 - - + -
108C PRO 3.6 4.0 - - - -
109C ILE* 3.9 12.1 - - + -
134C VAL* 3.5 30.1 - - + -
135C LYS* 1.3 71.9 - - - +
137C TYR* 1.3 61.4 + - - +
138C THR* 3.1 21.0 + - + +
142C ASN* 3.2 4.8 - - - -
143C TRP* 2.8 91.8 + + + +
145C LEU* 4.0 10.8 - - + -
279C PHE* 4.5 13.0 - + - -
316C LEU* 4.1 8.7 - - + -
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Residues in contact with TYR 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C PHE* 4.8 3.8 - + - -
107C THR* 3.5 7.2 - - - +
108C PRO* 3.0 30.8 + - + +
109C ILE 4.1 2.9 - - - -
110C ALA* 3.5 27.3 - - + +
135C LYS* 3.5 27.0 - - + +
136C PHE* 1.3 69.8 - - - +
138C THR* 1.3 59.1 + - - +
142C ASN* 3.1 27.6 - - - +
374C PRO 5.2 0.4 - - - -
375C VAL* 2.7 34.3 + - - +
377C CYS 3.4 23.1 - - - -
378C PRO* 4.5 0.4 - - + -
379C TYR* 3.8 26.0 - + + -
380C ARG* 2.8 39.4 + - + +
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Residues in contact with THR 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C LYS* 5.4 0.8 - - - +
99C VAL* 4.1 27.4 - - + -
107C THR* 4.1 5.8 - - + -
136C PHE* 3.5 25.1 - - + +
137C TYR* 1.3 76.5 - - - +
139C GLU* 1.3 68.3 + - - +
140C ASP* 2.8 19.5 + - - +
141C GLY* 2.6 39.4 + - - +
142C ASN* 4.7 0.7 + - - -
143C TRP* 4.4 9.4 - - + -
340C PRO* 4.7 5.8 - - + +
380C ARG* 3.4 13.7 - - - +
381C ALA* 3.9 0.3 - - - +
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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