Contacts of the strand formed by residues 97 - 102 (chain A) in PDB entry 3FWQ
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 LEU 97 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ILE* 4.1 7.9 - - - +
85A LEU* 3.8 37.8 + - + +
86A GLU* 3.9 25.6 - - + -
89A ARG* 2.8 38.5 + - + +
95A ILE 3.6 4.8 + - - -
96A THR* 1.3 71.6 - - - +
98A ALA* 1.3 57.4 + - - +
99A ASP 3.8 11.0 - - - +
100A ILE* 4.4 16.4 - - + -
111A LEU* 3.7 28.7 - - + -
112A VAL 3.6 13.9 - - - +
113A PHE* 3.8 18.6 - - + -
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Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TYR* 5.0 2.2 + - - +
65A VAL* 5.3 4.5 - - + -
89A ARG* 3.8 10.9 + - - +
97A LEU* 1.3 74.6 - - - +
99A ASP* 1.3 61.6 + - + +
112A VAL* 2.7 30.2 + - + +
113A PHE* 4.7 0.7 - - - -
114A GLU* 3.4 23.1 - - - +
61B ASN* 4.4 6.4 + - - -
63B GLU* 4.2 14.9 - - - +
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Residues in contact with ASP 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLU 5.3 0.3 - - - +
34A GLY* 3.2 18.0 + - - -
35A ASN 4.9 0.3 + - - -
39A TYR* 2.9 38.1 + - - +
97A LEU* 3.8 7.1 - - - +
98A ALA* 1.3 79.7 - - - +
100A ILE* 1.3 94.9 + - - +
101A VAL* 3.6 1.0 - - - +
111A LEU* 3.8 1.0 - - - -
112A VAL* 3.1 37.5 + - + -
60B THR* 5.2 1.4 + - - -
61B ASN* 3.5 27.5 + - - +
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Residues in contact with ILE 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A HIS* 5.8 0.2 - - + -
31A VAL* 3.8 9.0 - - + -
32A GLU* 3.7 21.0 + - + +
33A TRP* 3.4 27.3 - - + -
34A GLY 3.0 24.4 + - - -
82A ILE* 3.7 45.1 - - + -
86A GLU* 3.4 26.7 - - - +
97A LEU* 4.4 7.6 - - + -
99A ASP* 1.3 85.0 + - - +
101A VAL* 1.3 63.0 + - - +
109A PRO* 5.8 2.0 - - + -
110A ALA 3.7 8.1 - - - +
111A LEU* 4.3 6.1 - - + -
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TRP* 3.7 8.0 - - - -
34A GLY 3.6 18.2 - - - +
35A ASN 4.2 0.2 - - - +
36A GLN* 3.6 28.3 - - + +
39A TYR* 4.0 22.9 - - + -
99A ASP* 3.6 13.2 - - - +
100A ILE* 1.3 81.5 - - - +
102A LYS* 1.3 71.8 + - - +
103A ASP* 5.5 0.2 - - - -
109A PRO* 3.4 2.1 - - - +
110A ALA* 2.4 51.7 + - + +
112A VAL* 4.6 6.5 - - + -
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Residues in contact with LYS 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A TRP* 3.6 38.6 - - + -
36A GLN* 4.1 8.2 + - - +
78A ILE* 6.3 0.6 - - - +
101A VAL* 1.3 88.4 - - - +
103A ASP* 1.3 68.2 + - - +
104A PRO* 3.6 7.4 - - - +
107A ARG* 3.4 64.1 + - - +
108A THR 3.6 2.7 - - - +
109A PRO* 3.6 30.7 - - + +
110A ALA* 5.3 0.9 - - - -
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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