Contacts of the strand formed by residues 111 - 116 (chain A) in PDB entry 3BU0
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 LYS 111 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A TYR* 3.7 38.5 - - + -
92A PHE 5.3 6.3 - - - +
93A THR* 6.4 3.1 - - + -
108A VAL* 5.0 0.9 - - - -
110A ARG* 1.3 76.7 - - - +
112A GLN* 1.3 65.7 + - - +
158A ILE 3.6 0.2 - - - +
159A ASN* 3.4 4.0 - - - +
160A ARG* 2.8 63.0 + - + +
162A LYS* 6.5 1.8 - - - -
166A ASP* 5.8 0.7 - - - +
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Residues in contact with GLN 112 (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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91A TYR* 3.5 5.1 - - - +
92A PHE* 2.8 41.7 + - + +
96A LEU 5.0 2.5 - - - +
97A ALA* 5.4 0.6 - - - +
108A VAL* 4.1 21.4 - - + +
110A ARG* 3.5 20.0 - - - +
111A LYS* 1.3 76.7 - - - +
113A ALA* 1.3 62.4 + - - +
124A PHE* 3.3 39.1 - - - -
127A LEU* 4.2 8.5 - - - +
129A LEU* 4.2 4.7 - - + +
157A LEU* 4.3 16.0 - - + +
158A ILE 3.1 7.0 - - - +
159A ASN* 3.1 29.4 + - - +
301A AKG 5.1 1.0 + - - -
7B 2YR 5.1 1.0 + - - -
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Residues in contact with ALA 113 (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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89A VAL* 3.9 13.7 - - + -
90A GLU 3.4 26.2 - - - +
91A TYR* 4.0 3.4 - - + -
92A PHE* 3.8 8.1 - - + -
112A GLN* 1.3 75.3 - - - +
114A THR* 1.3 67.4 + - - +
115A TYR* 3.9 17.0 - - + -
132A LYS* 5.4 0.7 - - - +
156A VAL 3.9 0.2 - - - +
157A LEU* 3.6 1.6 - - - +
158A ILE* 2.8 36.5 + - + +
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Residues in contact with THR 114 (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 PHE* 3.4 11.3 - - - -
113A ALA* 1.3 80.1 - - - +
115A TYR* 1.3 59.2 + - - +
122A TYR* 4.5 1.3 - - + -
129A LEU* 3.9 24.2 - - + +
130A SER 3.0 23.7 + - - -
131A PRO* 3.4 3.6 - - - +
132A LYS* 2.7 36.7 + - - +
155A PHE* 3.6 31.9 - - + -
156A VAL 3.4 3.6 - - - +
157A LEU* 3.9 17.5 - - + -
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Residues in contact with TYR 115 (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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88A GLU 4.2 2.9 + - - -
89A VAL* 3.7 7.7 - - + -
90A GLU* 3.0 34.5 + - - +
113A ALA* 3.9 15.9 - - + -
114A THR* 1.3 78.6 - - - +
116A GLY* 1.3 56.6 + - - +
131A PRO* 3.9 4.5 - - - -
132A LYS* 3.2 29.6 - - + +
133A PRO 3.3 24.2 - - - +
134A TRP* 4.5 8.1 - - + -
135A ILE* 4.3 17.6 - - + +
138A LEU* 3.3 32.8 - - + -
155A PHE* 3.4 5.0 - - - -
156A VAL* 2.7 42.2 + - + +
158A ILE* 3.7 24.0 - - + -
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Residues in contact with GLY 116 (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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115A TYR* 1.3 77.1 - - - +
117A ASP* 1.3 67.8 + - - +
118A ALA 3.8 0.7 + - - -
131A PRO* 3.7 9.5 - - - +
132A LYS 3.0 18.5 + - - +
133A PRO* 4.2 4.0 - - - +
134A TRP* 3.3 26.0 + - - -
154A ASN 3.3 12.8 - - - -
155A PHE* 4.1 1.3 - - - -
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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