Contacts of the strand formed by residues 767 - 772 (chain G) in PDB entry 1M8V
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 VAL 767 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A ARG* 3.7 20.8 + - + +
166A ASN* 3.0 13.5 + - - -
719G VAL* 3.7 21.8 - - + -
720G ILE 3.9 3.6 - - - +
721G LEU* 4.2 0.9 - - + -
722G LYS* 3.5 10.8 - - - +
738G LEU* 4.5 6.5 - - + +
740G VAL* 5.1 1.6 - - + -
762G ILE* 4.0 12.8 - - + -
764G GLY* 3.1 27.0 + - - +
766G ASN* 1.3 81.2 - - - +
768G LEU* 1.3 65.8 + - - +
769G ALA* 3.3 30.1 - - - +
770G ILE* 3.9 14.1 - - + -
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Residues in contact with LEU 768 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 4.0 17.5 - - + -
123A LYS* 5.6 6.1 - - + -
125A PHE* 3.6 30.1 - - + -
127A PHE* 4.4 9.6 - - + -
162A ILE* 3.5 5.7 - - + +
163A ARG 3.0 22.2 + - - -
166A ASN* 3.1 40.7 + - + +
720G ILE* 2.7 43.4 + - + +
721G LEU 4.9 2.0 - - - +
722G LYS* 4.1 16.2 - - + +
766G ASN 3.9 0.6 + - - -
767G VAL* 1.3 76.5 - - - +
769G ALA* 1.3 58.2 + - + +
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Residues in contact with ALA 769 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A PHE* 5.3 1.1 - - + -
160A ILE* 3.6 27.8 - - + -
161A VAL 2.9 17.0 - - - +
162A ILE* 4.1 5.6 - - + -
163A ARG 4.6 0.2 - - - +
718G LEU 4.2 0.4 - - - -
720G ILE* 2.8 37.0 + - + -
767G VAL* 3.3 6.3 - - - +
768G LEU* 1.3 89.6 - - + +
770G ILE* 1.3 71.1 + - - +
771G SER 4.3 0.2 - - - -
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Residues in contact with ILE 770 (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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160A ILE* 4.3 0.9 - - - -
161A VAL* 2.8 45.4 + - + +
709G ILE* 4.2 29.8 - - + -
712G SER* 6.3 0.2 - - - -
717G VAL* 4.2 26.5 - - + -
718G LEU 3.0 8.1 - - - +
719G VAL* 4.4 11.9 - - + -
731G LEU* 5.8 3.6 - - + -
738G LEU* 4.9 11.4 - - + +
740G VAL* 3.8 28.5 - - + -
767G VAL* 3.9 15.9 - - + -
769G ALA* 1.3 82.0 - - - +
771G SER* 1.3 64.2 - - - +
772G PRO* 3.7 3.6 - - + +
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Residues in contact with SER 771 (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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157A TYR* 3.6 31.1 - - - +
158A GLY 5.0 0.5 + - - -
159A LYS 2.5 22.1 + - - -
160A ILE* 4.2 9.0 - - - -
717G VAL* 3.3 3.0 - - - -
718G LEU* 2.8 48.8 + - - +
720G ILE* 5.4 0.9 - - - +
770G ILE* 1.3 74.7 - - - +
772G PRO* 1.3 66.8 + - - +
773G THR 3.6 1.9 + - - -
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Residues in contact with PRO 772 (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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159A LYS* 3.3 31.1 + - + +
160A ILE* 4.6 0.4 - - - -
708G VAL* 3.6 25.1 - - + -
712G SER* 3.6 23.3 - - - +
715G LYS* 6.5 0.2 - - + -
717G VAL* 3.8 11.9 - - + -
770G ILE* 3.7 9.6 - - + +
771G SER* 1.3 90.3 + - - +
773G THR* 1.3 71.2 + - - +
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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