Contacts of the strand formed by residues 101 - 107 (chain A) in PDB entry 2BNN
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 ASP 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A LYS* 3.2 42.3 + - - +
95A GLY 4.1 2.8 - - - +
96A VAL* 4.4 10.9 - - - +
99A ASN 3.8 3.4 + - - -
100A VAL* 1.3 74.2 - - - +
102A TYR* 1.3 59.5 + - - +
103A TYR 4.0 6.6 - - - +
104A VAL* 4.4 2.9 - - - +
125A LEU* 3.3 35.3 - - + +
126A THR* 5.1 1.6 + - - -
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Residues in contact with TYR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A GLY 2.8 15.5 + - - +
97A ARG* 4.1 20.0 - - + -
100A VAL* 3.0 18.4 + - + +
101A ASP* 1.3 72.5 - - - +
103A TYR* 1.3 112.0 + + + +
125A LEU* 3.3 28.1 + - - +
126A THR* 3.4 28.7 + - + +
131A ASP 3.7 13.0 - - - -
132A ALA* 3.2 10.7 - - - +
133A LYS* 2.8 47.5 + - + -
182A PHE 2.7 24.1 + - - -
183A THR* 3.4 1.0 - - - +
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Residues in contact with TYR 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A GLY* 2.8 31.3 + - - +
97A ARG* 3.5 27.7 + - - -
101A ASP* 4.0 4.7 - - - +
102A TYR* 1.3 113.4 - + + +
104A VAL* 1.3 64.6 + - - +
105A TYR* 3.1 37.0 - + + -
122A VAL* 3.8 20.9 - - + -
123A ASP 3.5 3.8 - - - -
124A VAL* 4.2 20.4 - - + -
125A LEU* 3.9 1.6 - - - -
180A HIS 4.9 0.2 + - - -
181A ALA* 4.1 4.3 - - - -
182A PHE* 3.2 47.1 + + + -
1199A FCN 4.0 11.4 + + - -
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Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ILE* 3.8 28.0 - - + -
93A LEU 3.8 5.4 - - - +
94A LYS* 5.3 9.0 - - + +
101A ASP* 4.4 5.4 - - - +
103A TYR* 1.3 76.0 - - - +
105A TYR* 1.3 62.5 + - - +
106A ASN* 3.2 13.9 + - - +
121A VAL 3.6 0.5 - - - +
122A VAL* 3.6 0.9 - - - -
123A ASP* 2.9 54.2 + - + +
125A LEU* 3.7 24.9 - - + -
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Residues in contact with TYR 105 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A PRO 3.6 1.7 - - - +
92A ILE* 3.4 5.5 - - - +
93A LEU* 2.8 46.6 + - + +
94A LYS 4.0 8.3 - - - -
95A GLY* 3.7 21.9 - - - -
97A ARG* 3.7 9.5 + - - -
103A TYR* 3.1 33.9 - + + -
104A VAL* 1.3 71.4 - - - +
106A ASN* 1.3 60.7 + - - +
107A CYS* 3.8 2.8 + - - -
120A LEU* 4.1 19.3 - - + -
121A VAL 3.9 2.9 - - - -
122A VAL* 4.1 14.8 - - + -
1199A FCN 3.2 15.5 + - - -
23B LYS* 3.4 56.2 + - + -
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Residues in contact with ASN 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ARG* 3.9 34.2 + - + +
91A PRO 3.6 4.9 - - - +
92A ILE* 3.6 23.9 - - + +
104A VAL* 3.2 10.6 + - - +
105A TYR* 1.3 71.9 - - - +
107A CYS* 1.3 63.8 + - - +
108A LEU* 3.4 3.3 + - - +
120A LEU* 3.4 4.0 - - - -
121A VAL* 2.8 44.9 + - + +
123A ASP* 3.0 29.0 + - - +
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Residues in contact with CYS 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLN* 2.7 25.5 + - - -
90A ARG* 3.4 12.5 - - - +
91A PRO* 2.8 34.9 + - + +
93A LEU* 3.9 26.2 - - - -
105A TYR* 4.4 5.4 - - - -
106A ASN* 1.3 70.7 - - - +
108A LEU* 1.3 56.6 + - - +
110A ARG* 3.9 24.2 - - - +
119A PRO 4.1 3.6 - - - -
120A LEU* 3.9 19.1 - - + -
22B VAL 4.2 4.7 - - - -
23B LYS* 4.4 3.4 - - - -
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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