Contacts of the strand formed by residues 68 - 76 (chain G) in PDB entry 2P6T
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 LEU 68 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B LEU* 5.3 0.7 - - + -
117B MSE 4.3 21.1 - - + -
66G LEU 3.6 1.6 + - - -
67G GLY* 1.3 78.8 - - - +
69G GLN* 1.3 66.0 + - - +
70G ALA* 3.8 2.3 + - + +
113G PHE* 3.7 3.9 - - - -
114G PHE* 3.0 41.5 + - + +
116G ASP* 3.6 10.1 - - - +
117G MSE 3.4 51.4 - - + +
120G PHE* 4.6 7.0 - - + -
141G PHE* 3.7 41.3 - - + -
142G VAL 5.3 1.1 - - - +
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Residues in contact with GLN 69 (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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67G GLY 4.1 1.0 - - - -
68G LEU* 1.3 73.6 - - - +
70G ALA* 1.3 62.1 - - - +
71G PHE* 3.6 6.9 - - - -
111G GLN* 3.0 40.8 - - + +
112G ALA 3.5 6.5 - - - +
113G PHE* 3.3 41.9 - - + -
141G PHE* 3.5 4.2 - - - +
142G VAL* 2.9 51.0 + - + +
145G GLU* 4.6 4.5 - - - +
100H PHE* 3.4 31.2 - - - -
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Residues in contact with ALA 70 (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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68G LEU* 3.8 1.5 + - + +
69G GLN* 1.3 74.5 - - - +
71G PHE* 1.3 64.8 + - - +
72G ILE* 3.5 21.1 - - + +
110G LEU 3.6 0.7 - - - +
111G GLN* 3.6 5.4 - - - +
112G ALA 2.9 35.1 + - - +
114G PHE* 4.4 5.8 - - + -
120G PHE* 3.8 10.8 - - + -
140G SER 3.5 3.8 - - - -
141G PHE* 3.4 27.1 - - + -
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Residues in contact with PHE 71 (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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69G GLN* 3.7 10.5 - - - -
70G ALA* 1.3 71.6 - - - +
72G ILE* 1.3 63.2 + - - +
73G ARG* 3.9 5.0 + - - +
109G LEU* 4.3 26.9 - - + +
110G LEU 3.4 4.7 - - - -
111G GLN* 3.2 49.4 - - + -
138G GLN 4.1 0.7 - - - +
139G SER* 3.6 1.0 - - - -
140G SER* 2.7 31.8 + - - +
142G VAL* 3.8 10.3 - - + -
71H PHE* 5.0 7.2 - + - -
100H PHE* 3.5 34.5 - + - -
102H LEU* 3.3 35.4 - - + -
109H LEU* 4.2 15.9 - - + -
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Residues in contact with ILE 72 (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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1160A LEU* 5.3 0.4 - - - +
70G ALA* 3.5 35.2 - - + +
71G PHE* 1.3 72.1 - - - +
73G ARG* 1.3 66.2 + - - +
74G VAL* 3.6 27.0 + - + -
108G TYR 4.0 0.2 - - - +
109G LEU* 3.4 4.1 - - - +
110G LEU* 2.8 52.1 + - + +
112G ALA* 4.6 12.1 - - + -
114G PHE* 4.9 1.6 - - + -
120G PHE* 3.7 14.8 - - + -
123G PHE* 6.1 4.0 - - + -
124G VAL* 5.4 1.1 - - + -
128G LEU* 4.0 16.8 - - + -
137G ALA* 4.1 5.6 - - + -
138G GLN 3.7 5.8 - - - +
139G SER* 3.4 17.5 - - - -
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Residues in contact with ARG 73 (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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71G PHE 4.9 3.4 - - - +
72G ILE* 1.3 70.9 - - - +
74G VAL* 1.3 62.0 + - - +
105G GLU* 4.8 16.2 + - - +
106G THR* 3.7 28.7 - - - +
108G TYR 3.4 4.9 - - - -
109G LEU* 4.0 15.9 - - + -
136G ASP 4.0 0.3 - - - +
137G ALA* 3.3 2.1 - - - -
138G GLN* 2.7 73.6 + - + +
73H ARG* 3.0 46.0 - - - +
105H GLU* 6.0 2.6 - - - +
106H THR* 4.1 8.7 + - - -
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Residues in contact with VAL 74 (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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72G ILE* 3.6 24.2 + - + -
73G ARG* 1.3 73.0 - - - +
75G SER* 1.3 75.1 + - - +
76G ILE* 4.0 5.1 + - + +
86G PHE* 4.1 21.5 - - + -
106G THR* 5.0 0.7 - - - -
107G ASP* 3.6 6.5 + - - +
108G TYR* 2.9 38.9 + - + +
110G LEU* 4.5 7.9 - - + -
128G LEU* 3.6 28.5 - - + -
134G VAL* 4.0 14.8 - - + -
136G ASP 3.4 5.8 - - - +
137G ALA* 4.0 3.8 - - + -
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Residues in contact with SER 75 (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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136E ASP* 4.9 6.1 + - - -
73G ARG 4.2 0.2 + - - -
74G VAL* 1.3 76.6 - - - +
76G ILE* 1.3 69.9 + - - +
105G GLU 6.0 1.3 - - - -
107G ASP* 4.1 16.9 + - - +
135G GLN* 2.9 39.2 + - - +
136G ASP* 2.7 28.3 + - - +
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Residues in contact with ILE 76 (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 VAL* 4.0 4.2 + - + -
75G SER* 1.3 81.3 + - - +
77G ARG* 1.3 73.5 + - - +
82G ALA 3.8 20.2 - - - +
83G ARG* 4.0 27.1 - - + +
86G PHE* 3.3 49.1 - - + -
107G ASP* 4.1 19.1 + - - +
108G TYR* 3.6 18.1 - - + -
133G GLY 3.6 14.8 - - - +
134G VAL* 4.3 2.5 - - - +
135G GLN* 3.3 11.1 - - - +
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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