Contacts of the strand formed by residues 110 - 121 (chain C) in PDB entry 3BRW
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 110 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105C LEU* 3.6 10.8 - - - -
106C ASP* 2.8 37.1 + - - +
108C ALA 3.6 2.2 + - - -
109C LEU* 1.3 77.7 - - - +
111C HIS* 1.3 66.1 + - - -
112C LEU* 3.7 0.5 + - - +
134C LYS* 5.4 5.2 - - - -
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Residues in contact with HIS 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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104C SER 4.0 3.8 - - - -
105C LEU* 3.9 21.8 - - + +
109C LEU 3.9 0.6 + - - +
110C GLY* 1.3 73.7 - - - -
112C LEU* 1.3 70.5 + - - +
132C ARG 3.9 0.5 - - - +
134C LYS* 4.0 9.5 + - - +
391C ALA 5.5 1.3 - - - -
394C LEU* 3.7 32.1 - - + +
395C GLU* 3.5 42.2 + - + +
398C TYR* 3.6 45.1 - + + -
399C GLU* 4.7 6.3 - - - -
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Residues in contact with LEU 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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103C TYR* 3.2 10.0 - - - +
104C SER* 2.9 42.1 + - - +
106C ASP* 4.2 15.3 - - + +
109C LEU* 4.5 15.3 - - + -
110C GLY 4.1 6.1 - - - +
111C HIS* 1.3 84.0 - - - +
113C VAL* 1.3 66.3 + - - +
114C PHE 4.2 0.2 - - - -
131C LEU* 3.8 19.5 - - + -
132C ARG 3.5 11.7 - - - +
133C THR* 4.0 11.9 - - - -
164C VAL* 4.0 32.1 - - + -
166C VAL* 5.2 0.7 - - + -
169C PHE* 4.2 19.1 - - + -
394C LEU* 5.0 0.2 - - - -
398C TYR* 3.9 2.2 - - - -
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Residues in contact with VAL 113 (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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101C ASN* 5.7 0.9 - - + +
102C TYR 3.6 6.1 - - - +
103C TYR* 4.7 3.6 - - + -
112C LEU* 1.3 77.9 - - - +
114C PHE* 1.3 63.6 + - - +
132C ARG* 3.0 60.7 + - - +
172C VAL* 5.9 0.7 - - + -
181C ILE* 4.5 10.1 - - + -
394C LEU* 3.8 24.4 - - + +
397C LEU* 3.9 18.8 - - + -
398C TYR* 4.5 13.9 - - + -
401C LEU* 4.1 27.1 - - + -
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Residues in contact with PHE 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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100C PHE 3.9 0.3 - - - +
101C ASN* 3.4 3.2 - - - -
102C TYR* 2.7 46.5 + - + +
113C VAL* 1.3 75.2 - - - +
115C SER* 1.3 74.5 + - - +
116C LEU* 3.7 26.6 + - + -
129C LEU* 4.1 17.3 - - + -
130C LEU 3.3 27.1 - - - -
131C LEU* 3.7 21.3 - - + +
132C ARG* 4.3 0.2 - - - -
153C VAL* 3.9 22.7 - - + -
156C MET* 4.2 1.8 - - + -
157C ALA* 3.7 32.1 - - + -
160C VAL* 4.3 3.1 - - + -
169C PHE* 4.1 23.8 - + + -
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Residues in contact with SER 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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90C TYR* 3.2 12.7 - - - -
94C PHE* 3.8 21.3 - - - -
101C ASN* 2.6 22.9 + - - -
114C PHE* 1.3 75.4 - - - +
116C LEU* 1.3 63.3 + - - +
129C LEU 3.7 0.3 - - - -
130C LEU* 2.8 42.1 + - - +
132C ARG* 2.6 26.5 + - - +
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Residues in contact with LEU 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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175B PRO* 4.9 11.2 - - + -
94C PHE* 3.6 4.0 - - - -
99C HIS* 3.6 0.9 - - - +
100C PHE* 2.9 63.9 + - + +
102C TYR* 3.7 26.5 - - + +
114C PHE* 3.7 23.6 - - + -
115C SER* 1.3 75.3 - - - +
117C LYS* 1.3 62.6 + - - +
118C TYR* 6.1 0.2 - - + -
127C LEU* 5.8 0.7 - - + -
128C ARG 3.6 4.5 - - - -
129C LEU* 4.1 7.4 - - + -
153C VAL* 4.2 6.7 - - + -
156C MET* 3.6 38.6 - - + -
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Residues in contact with LYS 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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93C HIS* 3.3 43.4 + - + +
94C PHE* 3.5 22.6 - - + -
97C LYS* 4.3 18.4 - - + +
98C GLU 3.8 15.5 - - - +
99C HIS* 4.1 5.6 - - + +
100C PHE* 5.8 0.2 - - - -
116C LEU* 1.3 76.6 - - - +
118C TYR* 1.3 68.1 + - - +
119C ASP* 3.2 37.6 + - + +
127C LEU* 3.6 9.3 - - - +
128C ARG* 3.0 43.5 + - + +
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Residues in contact with TYR 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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175B PRO* 3.8 36.1 - - + -
176B LYS* 3.7 26.7 + - + +
179B ARG* 3.7 36.0 + - - -
98C GLU* 4.7 5.0 + - - +
100C PHE* 6.1 2.7 - - + -
116C LEU* 6.1 1.1 - - + -
117C LYS* 1.3 80.2 - - - +
119C ASP* 1.3 73.6 + - - +
120C VAL* 3.5 15.3 - - + +
125C GLU* 2.6 42.1 + - + -
126C HIS 3.5 15.9 - - - -
127C LEU* 4.1 13.0 - - + -
144C ILE* 5.0 4.0 - - + -
150C PHE* 4.1 11.9 - + - -
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Residues in contact with ASP 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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179B ARG* 5.0 2.5 + - - +
117C LYS* 3.2 33.5 + - + +
118C TYR* 1.3 82.7 - - - +
120C VAL* 1.3 71.3 + - - +
121C ILE* 3.6 26.4 + - + +
124C GLN 3.9 0.3 - - - +
125C GLU* 3.8 1.4 - - - -
126C HIS* 3.1 39.6 + - + +
127C LEU* 6.1 0.2 - - - -
128C ARG* 5.6 4.4 + - + +
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Residues in contact with VAL 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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179B ARG* 3.4 30.7 - - - +
118C TYR* 3.5 24.9 - - + +
119C ASP* 1.3 82.1 + - - +
121C ILE* 1.3 63.7 + - - +
122C GLY 3.5 22.7 + - - +
123C ASP* 4.8 4.7 - - - -
124C GLN 3.5 8.7 - - - +
125C GLU* 4.3 8.5 - - + -
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Residues in contact with ILE 121 (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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119C ASP* 3.6 25.7 - - + +
120C VAL* 1.3 71.3 - - - +
122C GLY* 1.3 60.7 + - - +
123C ASP 3.3 0.2 + - - -
124C GLN* 3.0 31.9 + - - +
126C HIS* 4.0 24.7 - - + +
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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