Contacts of the strand formed by residues 74 - 80 (chain S) 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 MET 74 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70S CYS* 3.0 22.0 + - + -
71S ASP* 3.1 18.4 + - + +
72S GLU 3.8 0.2 - - - -
73S HIS* 1.3 92.2 - - + +
75S GLY* 1.3 61.7 + - - +
92S LEU* 4.2 15.7 - - - -
96S CYS* 3.9 23.8 - - - -
107S LEU* 3.5 26.0 - - + +
108S ALA 3.9 1.3 - - - +
109S VAL* 3.7 16.4 - - + +
112S ALA* 3.6 31.6 - - + -
138S ILE* 4.5 9.4 - - + -
139S ILE 3.4 13.9 - - - +
140S GLY* 4.4 4.0 - - - -
221S PHE* 3.7 12.2 - - - +
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Residues in contact with GLY 75 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48S LEU* 4.5 0.4 - - - -
68S ILE 3.5 8.7 - - - -
70S CYS* 3.9 9.0 - - - -
74S MET* 1.3 77.0 - - - +
76S LEU* 1.3 64.0 + - - +
92S LEU* 6.1 0.2 - - - -
138S ILE* 3.4 6.0 - - - +
139S ILE 3.0 30.7 + - - +
221S PHE* 3.3 22.9 - - - -
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Residues in contact with LEU 76 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48S LEU* 3.5 10.5 - - - +
67S ILE* 3.3 6.1 - - - +
68S ILE* 3.0 71.5 + - + +
70S CYS* 4.1 10.8 - - - -
75S GLY* 1.3 73.7 - - - +
77S SER* 1.3 59.8 + - - +
78S LEU* 5.4 1.3 - - + +
89S SER* 3.9 27.1 - - - -
92S LEU* 4.2 12.1 - - + -
116S LEU* 5.3 0.9 - - + -
136S LEU* 4.0 35.0 - - + -
137S LEU 2.9 15.9 - - - +
138S ILE* 3.8 11.2 - - + -
221S PHE* 4.0 0.8 - - - -
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Residues in contact with SER 77 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37S THR* 3.0 29.4 + - - +
48S LEU* 3.5 16.3 - - - +
50S ALA* 4.4 2.2 - - - -
66S LYS 3.1 11.4 - - - -
67S ILE* 4.1 9.2 - - - -
76S LEU* 1.3 75.8 - - - +
78S LEU* 1.3 61.8 + - - +
135S GLY 3.8 0.2 - - - +
136S LEU* 3.2 8.9 - - - +
137S LEU* 2.8 51.4 + - - +
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Residues in contact with LEU 78 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37S THR* 4.2 5.8 - - - +
64S GLN* 4.6 4.7 - - - +
65S LYS 3.9 7.9 - - - +
66S LYS* 2.9 71.9 + - + +
68S ILE* 4.1 16.6 - - + -
76S LEU* 5.8 0.9 - - + -
77S SER* 1.3 74.7 - - - +
79S ALA* 1.3 65.2 + - - +
80S GLY 4.6 7.9 - - - +
82S ALA* 4.4 26.7 - - + +
85S ALA* 3.6 32.1 - - + -
134S VAL* 4.1 2.9 - - + -
135S GLY 3.5 5.2 - - - -
136S LEU* 4.0 5.8 - - + -
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Residues in contact with ALA 79 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31S ILE* 3.6 18.2 - - + +
34S GLY* 4.4 2.2 - - - -
35S SER 3.9 17.5 - - - +
37S THR* 4.4 2.5 - - + -
66S LYS* 3.8 4.9 - - - +
78S LEU* 1.3 76.4 - - - +
80S GLY* 1.3 59.0 + - - +
134S VAL* 3.8 2.4 - - - +
135S GLY 3.0 29.1 + - - -
165S ILE* 4.2 18.6 - - + -
166S GLY* 4.2 18.6 - - - +
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Residues in contact with GLY 80 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30S ALA* 3.6 22.9 - - - -
34S GLY* 4.0 10.9 - - - -
64S GLN* 5.8 1.0 + - - -
66S LYS* 5.0 0.6 - - - +
78S LEU* 4.6 6.5 - - - +
79S ALA* 1.3 74.9 - - - +
81S LEU* 1.3 64.9 + - - -
82S ALA* 3.3 4.2 + - - +
133S GLY 3.8 5.4 - - - -
134S VAL* 3.9 2.4 - - - +
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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