Contacts of the strand formed by residues 103 - 106 (chain P) in PDB entry 5FLX
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 ASN 103 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94P VAL 3.7 1.7 - - - +
95P GLY* 3.2 4.1 - - - -
96P VAL* 2.8 39.0 + - + +
98P ASN* 3.2 11.9 + - - +
101P THR* 2.9 23.2 - - - +
102P PHE* 1.3 72.9 - - - +
104P GLN* 1.3 62.5 + - - +
105P VAL* 3.8 9.0 + - + +
120P SER* 2.6 42.2 + - - +
121P ILE* 4.0 7.5 + - - +
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Residues in contact with GLN 104 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72P LYS* 4.8 12.2 + - - -
75P VAL* 3.3 44.3 - - + +
77P LYS* 5.0 9.3 - - + +
93P MET* 3.6 21.0 - - + +
94P VAL 4.2 2.9 - - - -
95P GLY* 4.7 1.1 - - - -
102P PHE* 4.6 8.1 - - + +
103P ASN* 1.3 73.7 - - - +
105P VAL* 1.3 63.8 + - - +
106P GLU 4.3 0.2 + - - -
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Residues in contact with VAL 105 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93P MET* 3.4 4.9 - - - -
94P VAL 3.5 23.4 + - - +
96P VAL* 5.5 1.6 - - + -
103P ASN* 3.8 10.3 + - + +
104P GLN* 1.3 80.2 - - - +
106P GLU* 1.3 73.8 + - - +
107P ILE* 3.4 9.0 + - - +
111P MET* 4.0 15.3 - - + -
119P PHE* 3.7 52.9 - - + +
118S ARG* 5.5 11.0 - - - +
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Residues in contact with GLU 106 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72P LYS* 6.5 1.3 - - - -
73P PRO* 5.7 7.7 - - + +
91P GLY* 5.2 7.6 - - - +
92P SER 3.8 14.6 - - - +
93P MET* 3.4 25.1 - - + +
105P VAL* 1.3 71.4 - - - +
107P ILE* 1.3 73.9 + - - +
108P LYS* 3.4 21.8 + - + +
111P MET* 3.3 19.6 - - - +
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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
------------------------------------------------------------
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