Contacts of the strand formed by residues 77 - 81 (chain P) in PDB entry 5C7O
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 THR 77 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75P GLU* 3.5 28.7 + - + +
76P LEU* 1.3 80.3 - - - +
78P VAL* 1.3 63.3 + - - +
100P LYS* 3.3 9.2 - - + -
102P VAL* 3.8 26.4 - - + +
161P VAL 4.7 2.0 + - - +
162P GLY 4.0 9.9 + - - +
163P SER 4.3 1.2 + - - -
164P PRO* 3.5 17.9 - - - +
165P TYR* 2.8 32.1 + - - +
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Residues in contact with VAL 78 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76P LEU* 4.2 10.1 - - + -
77P THR* 1.3 81.0 - - - +
79P GLY* 1.3 74.1 + - - +
80P ILE* 4.2 10.1 - - + -
94P CYS* 4.7 4.5 - - - -
99P VAL* 3.6 28.0 - - + -
100P LYS 2.9 10.4 + - - +
101P VAL* 3.4 16.4 - - + +
102P VAL* 2.8 29.7 + - - +
103P ALA 3.6 0.3 + - - -
164P PRO* 4.1 4.0 - - - -
165P TYR* 3.2 8.5 - - + +
167P VAL* 4.1 17.7 - - + -
400P LEU* 3.8 18.8 - - + -
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Residues in contact with GLY 79 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78P VAL* 1.3 78.5 - - - +
80P ILE* 1.3 58.1 + - - -
103P ALA 3.2 10.1 - - - -
158P TRP* 3.6 25.4 - - - -
164P PRO* 3.8 6.3 - - - +
165P TYR 2.9 8.8 + - - +
166P VAL* 3.3 3.0 - - - -
167P VAL 2.8 31.4 + - - -
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Residues in contact with ILE 80 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78P VAL* 4.2 10.5 - - + -
79P GLY* 1.3 77.3 - - - +
81P ASN* 1.3 60.7 + - - +
82P GLY 3.6 23.1 - - - +
83P PHE* 4.9 1.3 - - + -
87P GLY* 3.7 30.5 - - - +
90P VAL* 4.1 16.8 - - + -
91P LEU* 4.1 18.8 - - + +
101P VAL* 4.2 21.1 - - + -
103P ALA 2.9 10.4 + - - +
104P VAL* 3.3 15.3 - - + +
105P ASN 2.8 28.1 + - - +
158P TRP* 3.9 4.0 - - - -
167P VAL* 3.7 9.2 - - + +
169P SER* 3.8 5.4 - - - +
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Residues in contact with ASN 81 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79P GLY 4.2 0.4 - - - -
80P ILE* 1.3 70.8 - - - +
82P GLY* 1.3 60.2 + - - +
105P ASN* 2.7 31.4 + - - +
153P PRO* 4.4 8.1 - - - +
156P ILE* 3.4 11.0 - - - +
158P TRP* 4.4 7.3 - - + -
166P VAL* 4.6 0.2 - - + -
167P VAL 2.8 15.4 + - - +
168P GLU* 2.9 25.6 + - - +
169P SER* 2.8 34.5 + - - -
170P THR* 3.4 15.0 + - - +
173P TYR* 4.4 2.0 - - - -
182P HIS* 3.5 19.7 - - + -
501P NAD 3.3 10.9 + - - -
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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