Contacts of the strand formed by residues 91 - 96 (chain D) in PDB entry 3IFA
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 91 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 3.6 26.0 - - + -
85D LEU* 3.4 33.9 + - + +
86D GLN* 4.0 5.4 + - - +
89D TYR 3.6 0.6 - - - -
90D SER* 1.3 78.9 - - - +
92D CYS* 1.3 57.8 + - - +
93D VAL 4.6 0.9 - - - -
94D LEU* 4.1 17.4 - - + +
105D THR* 2.7 33.1 + - - +
109D LYS 3.7 0.4 + - - +
110D ARG* 3.3 9.0 - - - -
111D GLY 2.8 21.3 + - - -
113D TYR 3.2 8.1 - - - +
115D VAL* 4.2 6.1 - - + -
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Residues in contact with CYS 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D THR* 1.3 70.8 - - - +
93D VAL* 1.3 73.3 + - - +
104D ILE* 3.4 9.0 - - - +
105D THR* 2.8 31.4 + - - -
110D ARG* 3.6 16.2 - - + -
111D GLY 3.4 18.4 + - - +
112D LYS 4.2 1.1 - - - -
113D TYR 2.9 15.6 + - - -
114D VAL* 4.0 7.2 - - - -
141D LYS* 3.8 38.1 - - + -
147D PRO* 3.9 10.8 - - + -
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Residues in contact with VAL 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D THR 4.0 0.2 - - - -
92D CYS* 1.3 92.8 - - - +
94D LEU* 1.3 74.0 + - - +
102D ALA* 4.0 25.4 - - + -
103D ILE 3.3 7.0 - - - +
104D ILE* 4.5 4.3 - - + -
113D TYR 3.8 0.7 + - - +
114D VAL* 3.3 15.1 - - + +
115D VAL 3.1 22.7 + - - -
147D PRO* 3.8 19.7 - - + -
148D SER* 3.5 30.5 - - - +
151D ASP* 4.3 5.6 - - + +
152D ALA* 4.6 13.9 - - + -
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Residues in contact with LEU 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82D ILE* 4.1 33.9 - - + -
85D LEU* 3.6 28.5 - - + -
86D GLN* 4.2 20.4 - - + +
91D THR* 4.1 17.3 - - + +
93D VAL* 1.3 84.0 - - - +
95D VAL* 1.3 62.7 + - - +
102D ALA* 3.5 3.8 - - - +
103D ILE* 2.7 53.7 + - + +
105D THR* 4.9 2.5 - - - +
115D VAL* 3.2 19.7 - - + +
117D PHE* 4.0 15.0 - - + -
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Residues in contact with VAL 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D VAL* 4.8 0.2 - - + -
94D LEU* 1.3 77.3 - - - +
96D SER* 1.3 64.1 + - - +
101D ASP 6.1 0.2 - - - +
102D ALA* 4.0 17.7 - - + +
114D VAL* 5.7 0.2 - - - +
115D VAL 2.8 10.3 + - - -
116D CYS* 4.2 11.0 - - - -
117D PHE* 2.8 34.1 + - - +
152D ALA* 3.5 32.1 - - + -
278D LEU* 4.3 4.5 - - + -
279D TYR* 3.8 28.9 - - + -
310D ILE* 4.0 28.3 - - + -
311D HIS* 4.6 0.7 - - + -
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Residues in contact with SER 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D ASN* 2.7 22.9 + - - -
94D LEU 4.1 1.2 + - - -
95D VAL* 1.3 79.3 - - - +
97D GLU* 1.3 68.3 + - - +
98D GLU* 2.9 10.6 + - - +
99D ASN* 3.2 43.9 + - - +
101D ASP 5.3 1.4 + - - -
103D ILE* 4.6 6.1 - - - +
117D PHE* 3.4 22.7 - - - -
119D PRO* 3.9 3.5 - - - +
311D HIS* 3.3 7.1 - - - -
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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