Contacts of the strand formed by residues 102 - 107 (chain A) in PDB entry 4II9
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 ALA 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A LEU* 5.1 0.4 - - + -
68A LYS* 4.1 7.5 + - - +
69A LYS* 3.0 18.6 - - + +
71A ALA* 3.9 17.7 - - + -
98A LEU* 4.3 19.7 + - + +
100A GLY* 3.4 4.7 - - - +
101A ARG* 1.3 81.9 - - + +
103A TYR* 1.3 62.5 + - - +
104A VAL 3.7 15.7 - - - +
324A LEU* 3.5 17.3 - - + +
325A ASP* 4.5 1.4 + - - +
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Residues in contact with TYR 103 (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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64A THR* 3.9 8.5 - - + -
68A LYS* 3.9 9.6 - - + +
69A LYS 2.9 31.7 + - - -
70A PHE* 3.8 9.6 - - - -
102A ALA* 1.3 74.6 - - - +
104A VAL* 1.4 77.5 + - + +
323A VAL* 3.9 2.6 - - - +
324A LEU* 2.9 21.0 + - - -
325A ASP* 2.9 29.2 + - + +
328A VAL* 3.6 24.0 - - + -
329A TYR* 3.6 36.3 - + - -
332A LEU* 3.6 24.8 - - + +
333A VAL* 3.7 13.2 - - + +
101B UDP 2.7 37.3 + - - -
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Residues in contact with VAL 104 (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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70A PHE* 3.5 35.9 - - + -
71A ALA* 3.2 24.7 + - - +
102A ALA* 3.3 4.1 + - - +
103A TYR* 1.4 101.4 - - + +
105A LEU* 1.3 67.4 + - - +
106A ARG* 4.7 1.6 - - - +
321A ASP* 3.7 22.4 - - + +
322A LYS 3.4 15.5 - - - +
324A LEU* 4.2 6.1 - - - -
329A TYR* 3.6 26.2 - - + -
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Residues in contact with LEU 105 (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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57A MET* 3.8 15.7 - - + -
59A MET* 3.5 30.5 - - + -
71A ALA* 3.3 12.1 - - + +
72A TYR 4.5 0.2 - - - +
73A ALA* 4.5 1.8 - - + -
91A VAL* 4.3 19.5 - - + +
94A ALA* 3.5 31.2 - - + -
95A VAL* 4.7 2.5 - - + -
98A LEU* 4.1 14.1 - - + -
104A VAL* 1.3 73.3 - - - +
106A ARG* 1.4 68.8 + - - +
107A PHE* 4.2 9.2 - - + -
320A ILE 3.6 2.1 - - - +
321A ASP* 3.5 0.9 - - - -
322A LYS* 2.8 44.0 + - + +
324A LEU* 4.2 3.8 - - + +
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Residues in contact with ARG 106 (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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70A PHE* 3.8 31.2 - - + -
71A ALA 2.9 12.5 + - - +
72A TYR* 3.5 11.2 - - + -
73A ALA* 2.9 25.8 + - - +
104A VAL* 4.0 2.3 - - + +
105A LEU* 1.4 73.7 - - - +
107A PHE* 1.3 67.3 + - - +
129A ARG* 3.5 14.1 - - - +
142A ILE* 3.8 7.3 - - - +
319A GLU* 3.4 48.2 + - + +
320A ILE 3.4 4.7 - - - -
321A ASP* 2.7 39.7 + - - +
329A TYR* 4.7 0.4 - - - -
333A VAL* 3.9 22.2 - - - +
101B UDP 3.1 26.5 + - - -
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Residues in contact with PHE 107 (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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57A MET* 4.4 5.4 - - + -
73A ALA* 3.5 17.9 - - + +
76A GLY 3.4 16.2 - - - +
77A PRO* 3.6 16.6 - - + -
81A VAL* 4.5 1.6 - - + -
87A LEU* 3.8 22.4 - - + -
91A VAL* 3.9 24.0 - - + -
105A LEU* 4.2 19.3 - - + -
106A ARG* 1.3 79.3 - - - +
108A ASP* 1.3 60.9 + - - +
109A PRO* 3.4 8.9 - - + +
126A TYR* 3.9 18.4 - + - -
320A ILE* 2.8 76.8 + - + +
322A LYS* 4.9 1.3 - - + -
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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