Contacts of the strand formed by residues 109 - 118 (chain G) in PDB entry 3BZE
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 109 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101G CYS* 4.3 1.8 - - + -
102G GLU 3.9 5.4 - - - -
103G LEU* 3.6 6.9 - - - +
106G ASP* 5.6 0.3 - - - +
108G ARG* 1.3 80.3 + - - +
110G LEU* 1.3 64.5 + - - +
111G ARG* 3.2 24.7 - - - -
112G GLY* 3.2 26.0 - - - -
130G LEU* 4.2 10.5 - - + -
160G LEU 3.3 20.4 - - - -
161G GLU* 3.8 33.9 - - + +
165G VAL* 3.5 29.2 - - + +
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Residues in contact with LEU 110 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G SER* 5.3 5.2 - - - +
102G GLU* 2.9 20.1 + - + +
103G LEU 4.0 1.8 - - - +
104G GLY* 3.5 26.7 - - - +
105G PRO* 5.7 2.0 - - + -
108G ARG 3.0 1.2 + - - -
109G PHE* 1.3 82.3 - - - +
111G ARG* 1.3 97.2 + - + +
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Residues in contact with ARG 111 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G GLU* 2.2 73.2 + - - +
109G PHE* 3.2 17.8 - - - -
110G LEU* 1.3 109.5 - - - +
112G GLY* 1.3 71.4 + - - +
113G TYR* 4.0 13.8 - - + -
128G GLU* 6.1 1.3 - - - -
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Residues in contact with GLY 112 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100G GLY 3.3 10.5 - - - -
101G CYS* 4.2 0.7 - - - -
109G PHE* 3.2 16.8 - - - -
111G ARG* 1.3 83.5 - - - +
113G TYR* 1.3 66.3 + - - +
128G GLU* 5.1 3.3 - - - +
130G LEU* 3.7 19.2 - - - +
160G LEU* 4.3 8.5 - - - -
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Residues in contact with TYR 113 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G SER* 4.8 0.2 - - - -
6G LYS* 3.4 31.8 - - + +
98G MET* 5.3 13.5 - - + -
99G HIS* 3.2 5.4 - - - +
100G GLY* 2.9 55.6 + - - +
102G GLU* 2.9 39.7 + - + +
111G ARG* 4.0 16.6 - - + -
112G GLY* 1.3 78.4 - - - +
114G GLU* 1.3 65.3 + - - +
115G GLN* 6.0 4.9 - - + +
126G LEU* 5.2 1.8 - - - +
130G LEU* 4.6 3.4 - - - -
160G LEU* 3.9 9.2 - - - +
58H LYS* 5.3 13.0 + - - -
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Residues in contact with GLU 114 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G TRP* 3.3 33.0 + - + +
98G MET 3.4 5.6 - - - -
99G HIS* 3.8 14.5 - - + +
113G TYR* 1.3 80.7 - - - +
115G GLN* 1.3 67.5 + - - +
116G PHE* 4.3 2.1 - - - -
125G THR* 4.2 0.7 - - - +
126G LEU* 3.0 44.3 + - + +
133G TRP* 3.0 27.1 - - + -
156G GLN* 2.6 45.3 - - - +
160G LEU* 4.2 8.5 - - + +
7S LEU* 5.3 0.5 - - - +
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Residues in contact with GLN 115 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G TRP* 3.2 4.9 - - - -
98G MET* 2.8 59.0 + - + +
113G TYR* 6.0 4.7 - - + +
114G GLU* 1.3 76.5 + - - +
116G PHE* 1.3 68.1 - - - +
122G ASP* 4.9 7.8 + - - +
124G LEU 3.5 11.4 - - - +
125G THR* 2.8 36.2 + - - +
133G TRP* 5.4 0.2 - - - -
58H LYS* 5.4 4.7 - - - +
60H TRP* 3.4 25.9 - - + -
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Residues in contact with PHE 116 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74G PHE* 3.9 10.1 - + - -
95G LEU* 4.3 17.3 - - + -
96G GLN 3.1 6.5 - - - +
97G TRP* 3.4 47.3 - + + -
114G GLU* 4.6 0.2 - - - -
115G GLN* 1.3 78.6 - - - +
117G ALA* 1.3 62.3 + - - +
122G ASP* 3.9 1.0 - - - +
123G TYR* 2.9 28.1 + - + -
124G LEU* 2.8 37.3 + - + +
125G THR* 5.3 0.2 + - - -
133G TRP* 4.0 13.9 - + - -
60H TRP* 3.8 6.7 - - - -
6S THR* 3.8 16.2 - - - -
7S LEU* 3.8 36.8 - - + -
9S LEU* 4.4 13.2 - - + -
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Residues in contact with ALA 117 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94G THR 4.3 0.7 - - - -
95G LEU* 3.3 10.0 - - - +
96G GLN* 2.8 37.2 + - + +
116G PHE* 1.3 73.0 - - - +
118G TYR* 1.3 59.8 + - - +
120G GLY* 4.8 0.9 - - - -
121G LYS 3.3 15.9 - - - +
123G TYR* 4.0 3.1 - - - +
60H TRP* 3.3 47.8 - - + +
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Residues in contact with TYR 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78G LEU* 4.1 12.8 + - + -
81G LEU* 3.7 35.4 - - + -
82G ARG* 4.0 6.9 + - - +
85G TYR* 3.7 35.9 - + - +
87G GLN* 2.5 37.4 + - - -
93G HIS* 3.2 31.1 - - + +
94G THR 3.2 12.8 - - - -
95G LEU* 4.6 2.9 - - - -
117G ALA* 1.3 74.3 - - - +
119G ASP* 1.3 91.8 + - + +
120G GLY 3.1 1.3 - - - -
121G LYS* 3.0 23.5 + - - +
123G TYR* 3.9 16.2 - - + +
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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