Contacts of the strand formed by residues 41 - 47 (chain I) 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 VAL 41 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36I HIS* 3.1 3.2 - - - -
38I TYR* 2.8 42.2 + - + +
39I GLY 3.3 0.8 - - - -
40I HIS* 1.3 85.2 - - + +
42I PHE* 1.3 68.0 + - - +
74I ILE* 3.2 32.8 - - + +
75I GLU 3.9 1.1 - - - -
76I PRO* 3.7 29.6 - - + -
79I PHE* 3.5 39.0 - - + -
101I VAL* 4.4 3.8 - - + -
102I ALA 4.0 4.9 - - - +
103I GLY* 5.0 0.4 - - - -
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Residues in contact with PHE 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219H VAL* 4.9 1.6 - - + -
221H ILE* 4.4 10.3 - - + -
14I ILE* 4.2 15.7 - - + -
34I ILE* 3.9 14.4 - - + -
35I PHE 3.2 8.3 - - - -
36I HIS* 3.6 31.0 - + + -
40I HIS* 4.0 16.2 - - - -
41I VAL* 1.3 77.1 - - - +
43I LEU* 1.3 61.5 + - - +
44I GLY 4.3 0.2 - - - -
100I VAL 4.5 0.2 - - - -
101I VAL* 3.4 7.4 - - - +
102I ALA* 2.8 40.3 + - + +
176I TYR* 3.5 31.6 - + - -
178I ILE* 3.6 27.4 - - + -
184I VAL* 3.7 30.7 - - + -
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Residues in contact with LEU 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I ILE* 3.4 2.8 - - - -
35I PHE* 2.7 44.6 + - + +
38I TYR* 3.8 22.2 - - + +
41I VAL 4.1 0.6 + - - -
42I PHE* 1.3 75.1 - - - +
44I GLY* 1.3 66.4 + - - +
45I ILE* 3.9 18.8 - - + -
59I PHE* 3.6 32.3 - - + -
79I PHE* 3.9 17.0 - - + -
83I VAL* 4.7 3.8 - - + -
99I PRO* 3.9 18.2 - - + -
100I VAL 3.3 14.1 - - - +
101I VAL* 3.7 18.8 - - + -
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Residues in contact with GLY 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I VAL* 4.0 22.4 - - - -
14I ILE* 3.7 5.6 - - - +
33I LYS 3.0 9.4 - - - -
34I ILE* 4.0 7.6 - - - -
43I LEU* 1.3 75.6 - - - +
45I ILE* 1.3 63.3 + - - +
98I GLY 4.7 0.4 - - - -
99I PRO* 3.3 3.3 - - - +
100I VAL 2.7 36.5 + - - +
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Residues in contact with ILE 45 (chain I).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3I VAL* 4.1 1.2 - - - +
33I LYS* 2.7 36.5 + - - +
35I PHE* 4.0 15.7 - - + -
43I LEU* 3.9 28.0 - - + -
44I GLY* 1.3 78.8 - - - +
46I THR* 1.3 66.0 + - - +
52I VAL* 3.6 41.0 - - + +
55I LEU* 4.0 17.0 - - + -
56I ASN 4.1 3.4 - - - +
59I PHE* 5.4 0.4 - - + -
97I VAL* 3.6 37.2 - - + -
98I GLY 3.8 7.2 - - - +
99I PRO* 4.5 5.8 - - + -
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Residues in contact with THR 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1I GLY 5.8 0.4 - - - -
1I GLY 3.7 8.3 - - - +
2I ILE* 3.5 15.0 - - - +
3I VAL* 3.5 42.8 - - + +
33I LYS* 4.8 4.7 - - + -
45I ILE* 1.3 74.4 - - - +
47I GLY* 1.3 59.5 + - - +
52I VAL* 4.0 4.7 - - - -
97I VAL* 3.1 8.1 - - - +
98I GLY 2.7 31.7 + - - -
127I SER* 2.6 27.5 + - - +
128I GLY* 3.5 14.7 + - - -
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Residues in contact with GLY 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-6I PRO 4.5 4.3 - - - -
-5I SER* 4.7 18.6 - - - -
-2I ASN* 4.0 13.3 - - - +
-1I GLY 4.4 11.5 + - - +
46I THR* 1.3 79.6 - - - +
48I LEU* 1.3 67.0 + - - -
49I ALA* 3.2 5.4 + - - -
52I VAL* 4.1 2.6 - - - +
96I PHE 3.4 8.3 - - - -
97I VAL* 4.3 0.9 - - - -
98I GLY 4.9 0.2 - - - -
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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