Contacts of the strand formed by residues 74 - 80 (chain P) in PDB entry 3SDI
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 ILE 74 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70P LEU* 2.9 42.4 + - + -
71P ASN* 3.4 27.4 + - + +
73P LYS* 1.3 88.4 - - + +
75P ALA* 1.3 67.7 + - - +
107P ILE* 4.0 18.8 - - + +
109P VAL* 4.0 30.1 - - + -
112P LEU* 4.1 21.3 - - + -
138P TYR* 5.0 7.6 - - + -
139P ALA 3.3 12.3 - - - +
140P GLY* 4.2 7.9 - - - -
141P TYR 5.6 0.2 - - - +
221P GLN* 2.9 13.4 + - - +
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Residues in contact with ALA 75 (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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48P LEU* 4.1 17.7 - - + -
67P LEU* 6.3 0.4 - - + -
68P TYR 3.4 14.8 - - - +
69P LYS* 4.5 0.2 - - - -
70P LEU* 4.3 1.6 - - - +
74P ILE* 1.3 76.3 - - - +
76P VAL* 1.3 64.2 + - - +
138P TYR* 3.6 3.1 - - - -
139P ALA 2.8 32.5 + - - +
213P ALA* 5.6 6.1 - - + -
215P ILE* 4.2 7.4 - - + +
221P GLN* 3.7 15.5 - - - +
223P ILE* 5.9 4.5 - - + -
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Residues in contact with VAL 76 (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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48P LEU* 4.1 5.3 - - - +
66P LYS 3.6 0.5 - - - +
67P LEU* 3.5 5.7 - - - +
68P TYR* 2.9 51.4 + - + +
70P LEU* 3.9 25.4 - - + -
75P ALA* 1.3 77.3 - - - +
77P ALA* 1.3 59.4 + - - +
78P VAL* 4.7 2.7 - - + -
89P ILE* 4.4 4.3 - - + -
116P LEU* 5.7 0.4 - - + -
136P PHE* 4.0 26.0 - - + -
137P ILE 3.0 7.9 - - - +
138P TYR* 3.1 43.1 - - + -
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Residues in contact with ALA 77 (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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37P ALA* 3.9 22.4 - - + -
38P ILE 5.5 0.4 - - - +
48P LEU* 4.2 12.7 - - + +
49P ALA 5.3 1.1 - - - +
50P ALA* 5.1 0.2 - - + -
66P LYS 3.2 4.5 - - - -
67P LEU* 3.7 18.8 - - + -
76P VAL* 1.3 73.9 - - - +
78P VAL* 1.3 60.7 - - - +
135P SER 3.7 0.5 - - - +
136P PHE* 3.3 7.5 - - - -
137P ILE* 2.8 46.8 + - + +
165P VAL* 5.0 0.9 - - - +
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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
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37P ALA* 4.6 3.9 - - - +
65P GLU 4.6 6.7 - - - +
66P LYS* 2.8 52.6 + - + +
68P TYR* 4.1 20.0 - - + -
76P VAL* 4.7 2.7 - - + -
77P ALA* 1.3 74.7 - - - +
79P ALA* 1.3 71.1 + - - +
80P GLY 4.3 7.0 - - - +
81P LEU 5.0 0.4 - - - +
82P THR* 5.2 3.6 - - - +
85P ALA* 3.7 26.2 - - + -
89P ILE* 4.3 1.3 - - + -
134P VAL* 4.6 4.3 - - + -
135P SER 3.7 4.7 - - - +
136P PHE* 3.4 27.6 - - + -
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Residues in contact with ALA 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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31P ILE* 3.9 9.7 - - + +
34P ALA* 4.2 2.5 - - + -
35P GLY 4.1 9.0 - - - +
37P ALA* 5.3 0.7 - - + -
66P LYS* 3.9 4.9 - - - +
77P ALA 4.1 0.2 + - - -
78P VAL* 1.3 77.2 - - - +
80P GLY* 1.3 56.9 + - - +
134P VAL* 3.5 1.6 - - - +
135P SER 2.7 39.4 + - - +
165P VAL* 3.7 25.7 - - + +
166P GLY* 3.9 24.0 - - - +
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Residues in contact with GLY 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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30P SER* 5.7 1.6 - - - -
31P ILE* 4.2 9.6 - - - -
34P ALA* 3.5 19.8 - - - +
66P LYS* 4.9 1.7 + - - +
78P VAL* 4.2 4.6 - - - +
79P ALA* 1.3 75.0 - - - +
81P LEU* 1.3 67.8 + - - -
82P THR* 3.3 6.2 + - - -
133P GLY 3.2 10.5 - - - -
134P VAL* 4.3 1.8 - - - -
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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