Contacts of the strand formed by residues 108 - 120 (chain C) in PDB entry 5O67
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 PHE 108 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107C LYS* 1.3 82.9 + - - +
109C SER* 1.3 83.5 + - - +
110C PHE* 4.6 13.9 - + + -
156C GLY* 4.8 1.8 - - - -
157C ARG 3.4 11.7 - - - -
158C TYR* 4.1 18.6 - + + -
405C TYR* 4.2 3.5 - - - -
406C PHE* 3.4 67.6 + + + +
502C LDA 5.3 8.3 - - + -
504C C8E 4.2 24.0 - - + -
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Residues in contact with SER 109 (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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103C ALA* 5.5 1.7 - - - +
107C LYS 5.2 0.6 + - - -
108C PHE* 1.3 87.0 - - - +
110C PHE* 1.3 63.3 + - - +
111C GLU* 4.3 0.4 - - - +
156C GLY* 3.6 2.9 - - - -
157C ARG* 2.8 56.3 + - - +
403C PRO* 6.0 1.6 - - - -
404C TYR 3.3 15.5 - - - -
405C TYR* 4.0 26.6 - - - -
406C PHE* 4.3 0.9 - - - -
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Residues in contact with PHE 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C PHE* 4.6 7.2 - + + -
109C SER* 1.3 74.3 - - - +
111C GLU* 1.3 61.4 + - - +
112C THR* 3.5 23.3 + - - -
154C LEU* 4.0 27.8 - - + -
155C THR 3.3 20.2 - - - -
156C GLY* 4.5 5.4 - - - -
402C PHE 3.7 2.1 - - - +
403C PRO* 4.5 0.7 - - - -
404C TYR* 2.8 39.2 + - + +
406C PHE* 4.0 20.6 - - + -
502C LDA 3.7 44.2 - - + -
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Residues in contact with GLU 111 (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 PHE* 1.3 77.6 - - - +
112C THR* 1.3 73.2 + - - +
113C GLY* 4.6 1.3 - - - +
153C ASP 3.7 1.2 - - - +
154C LEU* 3.6 4.3 - - - -
155C THR* 2.8 45.6 + - - +
157C ARG* 2.7 35.6 + - - +
401C LYS* 3.1 35.5 - - + +
402C PHE 3.6 3.6 - - - -
403C PRO* 3.4 32.5 - - + +
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Residues in contact with THR 112 (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 PHE* 3.5 22.9 - - - -
111C GLU* 1.3 73.4 - - - +
113C GLY* 1.3 58.3 + - - +
152C LEU* 3.9 24.2 - - + -
153C ASP 3.5 2.7 - - - -
154C LEU* 4.0 12.0 - - + +
402C PHE* 2.8 50.8 + - + -
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Residues in contact with GLY 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C GLU* 4.1 2.2 - - - +
112C THR* 1.3 75.9 - - - +
114C ILE* 1.3 60.0 + - - -
115C THR* 5.3 2.0 - - - -
151C THR 3.7 1.1 - - - +
152C LEU* 3.4 10.3 - - - +
153C ASP* 2.8 42.2 + - - +
400C LEU 3.4 8.7 - - - -
401C LYS* 4.0 15.3 - - - -
402C PHE* 5.2 0.4 - - - -
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Residues in contact with ILE 114 (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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113C GLY* 1.3 73.6 - - - +
115C THR* 1.3 62.1 + - - +
150C TRP* 4.1 31.6 - - + -
151C THR 3.4 19.1 - - - +
152C LEU* 4.4 17.9 - - + +
398C PHE 4.2 0.2 - - - +
399C SER* 3.4 3.7 - - - -
400C LEU* 2.9 53.4 + - + +
401C LYS* 5.1 0.4 - - - +
402C PHE* 4.7 9.0 - - + -
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Residues in contact with THR 115 (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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113C GLY 5.3 0.3 - - - -
114C ILE* 1.3 77.8 + - - +
116C TYR* 1.3 63.1 + - - +
117C ALA* 4.7 3.4 - - + +
149C ASN 3.7 0.7 - - - +
150C TRP* 3.1 10.3 - - - +
151C THR* 2.8 47.4 + - - +
153C ASP* 4.7 7.0 + - - -
397C THR* 3.3 31.2 - - + -
398C PHE 3.5 6.3 - - - +
399C SER* 3.5 14.5 - - - -
401C LYS* 6.1 0.3 - - - +
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Residues in contact with TYR 116 (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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319B PHE* 6.1 2.7 - + - -
339B ASP* 4.4 6.3 - - - -
341B ILE* 5.6 3.2 - - + +
363B ASN* 3.6 17.7 + - - -
115C THR* 1.3 73.4 - - - +
117C ALA* 1.3 74.4 + - - +
118C ARG* 3.7 7.2 - - + -
148C ASP* 2.6 38.9 + - + -
149C ASN 3.4 9.0 - - - -
150C TRP* 3.8 44.6 - + + -
396C PHE* 3.8 29.6 - + - +
397C THR* 3.3 2.8 - - - -
398C PHE* 2.9 50.7 + + + +
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Residues in contact with ALA 117 (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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115C THR* 4.2 3.8 - - + -
116C TYR* 1.3 83.1 - - - +
118C ARG* 1.3 60.0 + - - +
119C TYR* 4.2 14.4 + - + +
147C ALA 4.1 0.3 - - - +
148C ASP* 3.8 1.7 - - - -
149C ASN* 2.8 39.1 + - + +
394C PRO* 4.3 10.3 - - + -
396C PHE 3.5 4.5 - - - +
397C THR* 3.9 20.9 - - + +
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Residues in contact with ARG 118 (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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363B ASN* 4.0 31.3 - - - +
390B THR* 4.3 11.3 - - + +
392B ASP* 5.2 1.4 + - - -
116C TYR* 3.7 9.0 - - - +
117C ALA* 1.3 74.8 - - - +
119C TYR* 1.3 72.2 + - - +
120C ASP* 3.3 31.5 + - - +
146C LYS* 4.0 18.0 - - - +
147C ALA 3.8 3.9 + - - -
148C ASP* 3.3 32.7 + - - -
394C PRO* 3.5 3.0 - - - +
395C ASP* 2.8 30.3 + - + +
396C PHE* 3.0 48.9 + - + +
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Residues in contact with TYR 119 (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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117C ALA* 4.5 11.4 - - + +
118C ARG* 1.3 79.7 + - - +
120C ASP* 1.3 61.1 + - - +
121C ALA* 4.1 6.3 - - + +
145C ILE 4.4 4.5 - - - +
146C LYS* 3.5 2.1 - - - -
147C ALA* 2.8 55.3 + - + +
149C ASN* 3.3 31.2 + - - -
175C ARG* 6.1 0.9 - - - -
392C ASP 5.8 1.1 - - - -
393C ALA* 4.2 6.3 - - - -
394C PRO* 3.6 45.0 - - + +
395C ASP 4.7 1.1 - - - +
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Residues in contact with ASP 120 (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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363B ASN 5.4 0.2 - - - +
390B THR* 5.2 3.0 - - - -
391B ASP* 4.6 24.5 + - - +
392B ASP* 4.1 19.1 - - - +
118C ARG* 3.3 26.5 + - - +
119C TYR* 1.3 73.5 - - - +
121C ALA* 1.3 64.1 + - - +
144C ARG* 5.1 7.8 - - - +
145C ILE 4.3 1.8 - - - -
146C LYS* 4.5 8.1 - - - +
395C ASP* 3.3 31.6 + - - +
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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