Contacts of the strand formed by residues 91 - 97 (chain A) in PDB entry 1FE3
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 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A VAL* 5.1 9.9 - - + -
4A PHE* 3.9 40.8 - - + -
42A ILE* 5.0 13.5 - - + -
51A ILE* 5.2 11.2 - - + -
64A PHE* 5.2 4.0 - - + -
66A LEU* 5.5 4.9 - - + -
84A VAL* 3.3 34.8 - - + -
85A SER 3.6 8.7 - - - +
86A LEU* 4.7 5.6 - - + -
89A ASP 3.9 0.2 + - - -
90A LYS* 1.3 72.5 - - - +
92A VAL* 1.3 61.5 + - - +
93A HIS* 5.1 2.8 - - + +
104A PHE 3.3 3.8 - - - +
105A VAL* 3.5 1.1 - - - -
106A ARG* 3.0 46.5 + - + +
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Residues in contact with VAL 92 (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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84A VAL* 3.1 5.6 - - - +
85A SER* 2.8 49.7 + - - +
87A ASP* 3.2 42.8 - - + +
90A LYS* 5.0 1.8 - - + -
91A LEU* 1.3 72.7 - - - +
93A HIS* 1.3 60.4 + - - +
94A ILE* 4.1 16.1 - - + +
103A ASN* 5.6 1.1 - - + +
104A PHE 3.6 2.2 - - - -
105A VAL* 4.0 31.2 - - + -
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Residues in contact with HIS 93 (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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51A ILE* 5.4 2.9 - - + -
62A ILE* 4.0 22.5 - - + +
70A PHE* 5.0 0.2 - + - -
72A GLU* 2.8 31.3 + - - -
82A SER* 3.6 10.5 - - - -
83A VAL 3.7 5.6 + - - -
84A VAL* 3.9 16.4 - - + -
91A LEU* 5.1 3.1 - - + +
92A VAL* 1.3 74.5 - - - +
94A ILE* 1.3 64.7 + - - +
95A GLN* 3.6 16.1 + - + +
103A ASN* 3.3 3.3 - - - +
104A PHE* 2.8 61.7 + + + +
106A ARG* 4.0 22.2 - - - +
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Residues in contact with ILE 94 (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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82A SER* 3.2 8.0 - - - -
83A VAL* 2.8 41.4 + - + +
92A VAL* 5.0 14.8 - - + -
93A HIS* 1.3 75.4 + - - +
95A GLN* 1.3 63.2 + - - +
96A LYS* 3.4 33.0 - - + +
101A GLU* 4.2 16.8 - - - +
102A THR 3.6 6.3 - - - +
103A ASN* 3.5 24.9 - - + +
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Residues in contact with GLN 95 (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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72A GLU* 2.8 19.9 - - - +
74A THR* 3.2 19.7 - - - +
78A ARG* 2.5 40.7 + - - +
80A CYS* 4.0 6.7 - - + -
82A SER* 3.1 20.4 - - - +
93A HIS* 3.6 10.2 + - + +
94A ILE* 1.3 71.4 - - - +
96A LYS* 1.3 62.5 + - - +
97A TRP* 3.4 6.2 - - - -
101A GLU* 3.6 1.0 - - - -
102A THR* 2.8 45.3 + - + +
104A PHE* 3.6 26.1 - - + -
133A OLA 5.1 2.3 - - - +
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Residues in contact with LYS 96 (chain A).
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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69A GLU* 5.0 10.1 - - - -
80A CYS* 3.2 4.8 - - - +
81A LYS* 2.8 61.0 + - + +
83A VAL* 4.3 16.5 - - - +
94A ILE* 3.4 23.4 + - + +
95A GLN* 1.3 76.2 - - - +
97A TRP* 1.3 60.7 + - - +
100A LYS 3.9 4.5 - - - +
101A GLU* 3.3 33.7 - - + +
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Residues in contact with TRP 97 (chain A).
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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23A LEU* 3.9 20.6 + - + -
78A ARG* 3.4 53.8 - - + +
79A ASN 3.3 24.9 - - - +
80A CYS* 3.8 7.0 - - - -
95A GLN 3.4 21.3 - - - -
96A LYS* 1.3 73.5 - - - +
98A ASP* 1.3 83.0 + - - +
99A GLY 3.5 1.8 - - - -
100A LYS* 3.1 33.5 + - + +
101A GLU* 3.5 12.3 - - - -
102A THR* 3.5 16.8 - - + -
119A PHE* 3.6 25.6 - + - -
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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