Contacts of the strand formed by residues 99 - 103 (chain A) in PDB entry 5G04
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 MET 99 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A CYS* 3.8 33.1 - - - +
31A HIS* 3.4 40.2 - - + +
33A ASN* 3.2 48.9 - - + +
94A TYR 4.2 0.3 - - - +
96A ALA* 3.4 31.0 + - - +
97A GLY 3.2 2.3 - - - +
98A ASN* 1.3 83.5 + - - +
100A VAL* 1.3 61.1 + - - +
101A ILE* 4.1 8.2 + - + -
117A PHE 3.3 6.1 - - - +
118A THR* 3.5 18.4 - - + +
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Residues in contact with VAL 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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93A LEU* 3.7 25.6 - - + -
94A TYR 3.1 15.0 - - - +
95A VAL* 4.0 7.4 - - + -
99A MET* 1.3 70.5 - - - +
101A ILE* 1.3 63.5 + - - +
116A ALA* 3.7 0.2 - - - -
117A PHE* 2.5 44.2 + - - +
123A VAL* 3.8 25.4 - - + -
126A ALA* 3.6 26.7 - - + -
151A ILE* 4.0 5.4 - - + -
153A ILE* 3.5 24.5 - - + -
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Residues in contact with ILE 101 (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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23A PHE* 5.3 0.9 - - + -
24A GLY* 4.0 18.2 - - - -
27A HIS* 3.8 22.9 - - + +
28A CYS* 3.3 35.4 - - - +
31A HIS* 4.9 2.5 - - - +
93A LEU* 3.5 5.9 - - - +
94A TYR* 2.9 36.1 + - + +
99A MET* 4.1 10.5 - - + -
100A VAL* 1.3 76.8 - - - +
102A TRP* 1.3 63.2 + - - +
103A SER* 3.4 19.0 + - - +
113A VAL* 3.5 25.6 - - + -
115A LYS 3.8 2.0 - - - -
116A ALA* 4.0 17.5 - - + -
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Residues in contact with TRP 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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77A ARG* 4.3 6.1 - - - -
91A GLU* 2.8 41.1 + - + -
92A GLU 3.5 10.3 - - - -
93A LEU* 3.8 9.9 - - + -
101A ILE* 1.3 72.9 - - - +
103A SER* 1.3 60.1 + - - +
104A LYS* 5.1 0.4 - - - -
113A VAL* 3.8 1.9 - - - +
114A TYR* 2.7 67.7 + + + +
115A LYS* 3.1 24.8 + - - +
117A PHE* 3.8 22.4 - + + -
128A TRP* 3.7 27.9 - + - -
149A LYS 4.9 2.2 - - - -
151A ILE* 3.9 23.1 - - + -
162A HIS* 5.1 3.1 - - - -
164A ILE* 3.4 31.2 - - + -
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Residues in contact with SER 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 4.3 14.6 - - - -
24A GLY 4.4 5.5 + - - -
91A GLU* 3.2 6.9 - - - +
92A GLU* 2.7 64.1 + - - +
94A TYR* 4.9 2.8 - - - +
101A ILE* 3.4 23.6 + - - +
102A TRP* 1.3 77.1 - - - +
104A LYS* 1.3 63.0 + - - +
105A GLY 4.0 0.2 - - - -
111A LEU* 5.5 0.2 - - - -
112A ALA 3.4 9.2 - - - -
113A VAL* 4.7 0.2 - - - -
114A TYR 4.1 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