Contacts of the strand formed by residues 66 - 72 (chain G) in PDB entry 3P1M
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 66 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64G GLU 5.1 2.0 - - - +
65G ASP* 1.3 81.6 - - - +
67G ILE* 1.3 67.3 + - - +
82G LYS* 4.5 36.5 + - + +
83G GLY* 3.3 14.1 - - - +
84G LYS* 3.7 39.7 - - + +
161G ASP* 4.8 0.3 - - - +
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Residues in contact with ILE 67 (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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65G ASP* 5.3 0.4 - - + -
66G LYS* 1.3 79.8 - - - +
68G THR* 1.3 61.3 + - - +
69G VAL* 3.9 7.0 + - + +
82G LYS* 3.2 7.5 - - - +
83G GLY 2.7 46.8 + - - +
85G VAL* 3.9 20.9 - - + -
156G LEU* 3.9 28.5 - - + -
157G THR 3.7 6.5 - - - +
158G LYS* 4.4 16.8 - - + +
160G MET* 3.7 40.4 - - + +
161G ASP* 3.2 23.3 - - + +
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Residues in contact with THR 68 (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 ILE* 1.3 72.7 - - - +
69G VAL* 1.3 65.4 + - - +
70G HIS* 3.9 8.7 - - + -
80G THR* 3.7 24.2 - - + -
81G THR 3.4 11.7 - - - +
82G LYS* 3.7 21.5 - - + +
160G MET 3.8 1.0 - - - +
161G ASP* 2.7 18.9 + - - -
162G ASN* 2.6 50.9 + - - +
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Residues in contact with VAL 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 ILE* 3.9 11.2 + - + +
68G THR* 1.3 80.8 - - - +
70G HIS* 1.3 72.9 + - - +
71G PHE* 3.6 25.2 + - + -
79G LEU 3.9 0.7 - - - +
80G THR* 3.8 0.3 - - - -
81G THR* 3.0 39.1 + - + +
83G GLY 5.3 1.8 - - - +
89G LEU* 4.1 7.9 - - + -
92G VAL* 5.3 2.9 - - + -
156G LEU* 3.8 33.7 - - + -
163G MET* 3.7 27.1 - - + +
165G VAL* 4.4 2.9 - - + -
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Residues in contact with HIS 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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189F TYR* 3.3 47.3 - + + -
68G THR* 3.9 7.8 - - + +
69G VAL* 1.3 74.7 - - - +
71G PHE* 1.3 60.2 + - - +
78G THR* 4.3 14.1 - - + +
79G LEU 3.5 2.9 - - - -
80G THR* 2.7 42.0 + - + +
162G ASN* 3.3 28.9 + - - -
163G MET 2.9 19.0 + - - +
164G THR* 3.2 16.0 - - + +
165G VAL* 2.9 29.3 + - - +
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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 VAL* 3.6 20.4 - - + -
70G HIS* 1.3 76.3 - - - +
72G ILE* 1.3 65.4 + - - +
73G ASN 3.8 0.6 + - - +
77G GLU 3.6 0.7 - - - +
78G THR* 3.3 4.8 - - - +
79G LEU* 2.8 55.4 + - + +
81G THR* 3.9 19.5 - - + -
89G LEU* 3.9 22.7 - - + -
92G VAL* 4.1 8.5 - - + -
93G VAL* 3.7 30.1 - - + -
98G LEU* 3.9 13.7 - - + -
100G ILE* 4.3 13.9 - - + -
117G LEU* 4.6 9.0 - - + -
165G VAL* 3.4 23.8 - - + -
167G VAL* 4.5 11.0 - - + -
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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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183A THR* 3.9 22.2 - - + +
184A SER* 4.6 10.3 - - - -
191D GLN* 4.8 5.6 - - - +
188F LEU* 4.9 4.3 - - + -
71G PHE* 1.3 72.9 - - - +
73G ASN* 1.3 70.7 + - - +
76G GLY* 4.3 17.3 - - - +
77G GLU 3.7 2.9 - - - -
78G THR* 4.3 16.2 - - + +
164G THR* 3.8 27.1 - - + -
165G VAL 2.9 11.0 + - - +
166G ARG* 3.8 19.0 - - + +
167G VAL* 2.9 29.8 + - - +
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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