Contacts of the helix formed by residues 96 - 106 (chain L) in PDB entry 6PSU
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 ASP 96 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313J GLY* 5.4 5.5 - - - -
314J ARG* 4.5 18.0 - - - +
39L ASP* 4.9 9.2 + - - +
94L THR* 3.4 18.3 - - + +
95L THR* 1.3 74.1 + - - +
97L PRO* 1.3 66.8 - - + +
98L VAL* 3.0 11.0 - - + -
99L ARG* 2.8 47.0 + - + +
100L MET* 2.8 12.3 + - - +
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Residues in contact with PRO 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294J ASN* 4.6 2.6 - - - +
297J ARG* 3.5 37.3 + - + +
298J MET* 4.9 5.4 - - + -
301J GLU* 4.0 29.4 - - + -
312J ARG* 5.5 3.4 - - - +
95L THR 3.0 10.3 - - - +
96L ASP* 1.3 81.8 - - + +
98L VAL* 1.3 58.1 + - + +
100L MET* 3.8 4.1 - - + +
101L TYR* 2.9 28.9 + - - +
402L LEU* 3.5 23.9 - - + +
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Residues in contact with VAL 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96L ASP* 4.1 13.5 - - + -
97L PRO* 1.3 75.9 - - + +
99L ARG* 1.3 72.1 + - + +
101L TYR* 3.1 2.0 + - - +
102L MET* 2.9 50.4 + - + +
401L PHE* 3.6 23.8 - - + -
402L LEU* 3.3 38.6 - - + -
405L ILE* 5.7 0.2 - - + -
57O T 5.7 9.4 - - + +
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Residues in contact with ARG 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39L ASP* 4.4 8.3 + - - -
94L THR* 3.9 26.9 - - + -
96L ASP* 2.8 33.9 + - + +
98L VAL* 1.3 79.6 - - + +
100L MET* 1.3 56.7 + - + +
102L MET* 3.3 9.2 + - - +
103L ARG* 2.9 40.6 + - + +
57O T 3.4 37.1 + - - +
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Residues in contact with MET 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J TYR* 3.2 35.2 - - + +
142J GLU* 3.7 14.1 - - - +
297J ARG* 3.2 47.2 + - - +
94L THR 4.1 8.1 - - - +
95L THR* 3.2 39.3 - - + +
96L ASP 2.8 15.9 + - - +
97L PRO 4.0 1.1 - - - +
99L ARG* 1.3 73.0 - - - +
101L TYR* 1.3 57.9 + - - +
103L ARG* 3.4 17.5 + - - +
104L GLU* 2.9 27.7 + - - +
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Residues in contact with TYR 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290J ILE* 4.7 15.0 - - + -
291J ILE* 4.7 3.8 - - - +
294J ASN* 3.1 41.5 - - + +
297J ARG* 4.2 4.9 - - - +
97L PRO 2.9 21.0 + - - +
98L VAL* 3.5 7.0 - - - +
99L ARG 3.1 0.4 - - - -
100L MET* 1.3 75.0 - - - +
102L MET* 1.3 72.7 + - + +
104L GLU* 3.3 9.8 + - + +
105L MET* 2.9 51.2 + - + +
384L LEU* 3.2 24.9 - - + +
387L VAL* 5.6 1.1 - - + +
388L ILE* 4.5 10.1 - - + -
402L LEU* 5.2 1.6 - - + -
405L ILE* 4.4 20.0 - - + -
406L GLN* 4.6 3.4 + - - -
409L ASN* 3.7 16.7 + - - -
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Residues in contact with MET 102 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98L VAL* 2.9 40.4 + - + +
99L ARG* 3.7 8.1 - - - +
101L TYR* 1.3 91.5 - - + +
103L ARG* 1.3 58.0 + - + +
105L MET* 3.0 8.7 + - - +
106L GLY* 2.9 26.0 + - - -
388L ILE* 4.7 13.7 - - + -
401L PHE* 4.3 18.4 - - + -
405L ILE* 6.1 1.3 - - + -
55O C 4.0 36.6 + - + +
56O C 5.7 2.2 - - - +
57O T 4.4 24.7 - - + +
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Residues in contact with ARG 103 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142J GLU* 3.7 23.7 + - - +
94L THR* 2.9 42.2 + - - +
99L ARG* 2.9 22.6 + - + +
100L MET* 3.8 21.1 - - - +
102L MET* 1.3 77.0 - - + +
104L GLU* 1.3 61.5 + - - +
106L GLY* 3.2 12.7 + - - +
107L THR* 4.7 2.8 + - - +
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Residues in contact with GLU 104 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141J PHE 5.1 5.5 - - - +
290J ILE* 3.1 49.3 - - + +
293J ARG* 5.9 8.5 + - - +
297J ARG* 4.7 12.7 + - - +
100L MET 2.9 17.5 + - - +
101L TYR* 3.4 16.2 - - + +
102L MET 3.2 0.2 - - - -
103L ARG* 1.3 77.6 - - - +
105L MET* 1.3 57.9 + - - +
106L GLY 3.1 5.0 + - - -
107L THR* 3.9 14.7 + - - +
108L VAL* 4.4 3.5 - - - +
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Residues in contact with MET 105 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290J ILE* 6.4 0.2 - - + -
101L TYR* 2.9 42.1 + - + +
102L MET* 3.0 8.5 + - - +
104L GLU* 1.3 75.0 - - + +
106L GLY* 1.3 63.8 + - - +
107L THR 3.3 0.9 - - - -
108L VAL* 2.9 40.9 + - + +
384L LEU* 3.3 43.7 - - + -
385L ARG* 3.7 29.1 + - - +
388L ILE* 3.4 23.3 - - + -
55O C 4.1 6.4 - - - +
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Residues in contact with GLY 106 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102L MET 2.9 11.9 + - - -
103L ARG* 3.2 8.6 + - - -
104L GLU 3.1 3.6 - - - -
105L MET* 1.3 78.3 - - - +
107L THR* 1.3 58.9 + - - +
108L VAL 3.1 9.9 + - - +
385L ARG* 6.0 0.4 + - - -
55O C 4.6 14.4 + - - -
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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