Contacts of the helix formed by residues 94 - 106 (chain L) in PDB entry 6IY6
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 SER 94 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92L CYS 3.7 1.8 + - - -
93L ASP* 1.3 76.7 + - - +
95L PHE* 1.3 62.7 + - - +
96L THR* 3.3 8.5 - - - +
97L SER* 3.3 20.1 + - - -
98L THR* 3.3 14.7 + - - -
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Residues in contact with PHE 95 (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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88L LYS 4.9 2.5 - - - -
89L LEU* 3.9 19.7 - - + -
91L SER 4.3 4.9 - - - -
92L CYS* 3.7 22.1 + - - +
93L ASP 3.2 2.2 - - - -
94L SER* 1.3 73.2 - - - +
96L THR* 1.3 61.4 + - + +
97L SER 3.2 0.7 - - - -
98L THR* 3.2 7.5 + - - -
99L ILE* 2.9 62.0 + - + +
128L LEU* 4.0 2.5 - - + -
131L ASN* 3.3 34.3 - - + -
133L ALA* 4.1 15.0 - - + -
134L TRP* 3.8 35.0 - - + -
137L GLN* 4.1 19.7 - - - -
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Residues in contact with THR 96 (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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94L SER* 4.3 8.0 - - - -
95L PHE* 1.3 78.3 + - + +
97L SER* 1.3 54.7 + - - -
99L ILE* 3.5 10.1 - - - +
100L ASN* 2.7 36.5 + - - -
137L GLN* 4.5 14.6 - - - +
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Residues in contact with SER 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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94L SER* 3.3 17.4 + - - -
95L PHE 3.2 0.4 - - - -
96L THR* 1.3 79.6 + - - +
98L THR* 1.3 65.7 + - - +
100L ASN* 3.1 18.8 + - - +
101L GLU* 3.2 12.4 + - - +
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Residues in contact with THR 98 (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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84L PHE* 3.7 19.9 - - + -
88L LYS* 3.5 51.3 + - + +
89L LEU* 3.9 14.6 - - + -
93L ASP 4.4 3.6 + - - -
94L SER* 3.3 12.7 + - - -
95L PHE* 3.2 13.0 + - + -
97L SER* 1.3 77.1 - - - +
99L ILE* 1.3 62.0 + - - +
101L GLU* 3.2 20.7 + - - +
102L LEU 3.3 9.0 + - - -
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Residues in contact with ILE 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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89L LEU* 4.9 1.6 - - + -
95L PHE* 2.9 33.7 + - + +
96L THR 3.5 11.4 - - - +
98L THR* 1.3 76.9 - - - +
100L ASN* 1.3 63.3 + - - +
102L LEU* 3.3 12.3 + - + +
103L ASN* 2.9 31.6 + - - +
128L LEU* 3.8 20.0 - - + -
134L TRP* 3.7 27.4 - - + -
137L GLN* 4.0 21.5 - - - +
144L PRO* 4.0 22.0 - - + -
147L VAL* 3.8 12.8 - - + +
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Residues in contact with ASN 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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96L THR* 2.7 24.6 + - - +
97L SER* 3.1 11.0 + - - +
99L ILE* 1.3 80.0 - - - +
101L GLU* 1.3 59.3 + - - +
103L ASN* 3.5 9.7 + - - +
104L HIS* 3.1 27.5 + - - +
144L PRO* 3.7 19.4 - - - +
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Residues in contact with GLU 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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206J PRO 5.6 0.3 - - - +
208J GLU* 3.1 29.2 - - - +
80L HIS* 4.3 7.8 + - - -
81L TRP* 5.1 0.7 - - + -
84L PHE* 3.7 21.8 - - + -
88L LYS* 3.5 20.1 + - - +
97L SER 3.2 10.5 + - - +
98L THR* 3.2 12.4 + - - +
100L ASN* 1.3 75.2 - - - +
102L LEU* 1.3 57.1 + - - +
104L HIS* 3.3 9.0 + - - +
105L CYS* 3.0 42.7 + - - -
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Residues in contact with LEU 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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81L TRP* 3.6 30.3 - - + -
84L PHE* 4.2 8.0 - - + -
89L LEU* 4.5 10.5 - - + -
98L THR 3.3 8.9 + - - +
99L ILE* 3.5 16.4 - - + +
101L GLU* 1.3 76.6 - - - +
103L ASN* 1.3 62.5 + - - +
105L CYS* 3.6 4.4 + - - +
106L LEU* 3.2 35.2 + - + +
112L LEU* 4.0 16.2 - - + -
124L VAL* 3.8 28.9 - - + -
128L LEU* 4.2 19.1 - - + -
147L VAL* 4.0 11.7 - - + -
150L TRP* 4.6 2.5 - - + -
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Residues in contact with ASN 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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99L ILE 2.9 16.4 + - - +
100L ASN* 3.5 11.7 + - - +
101L GLU 3.2 0.2 - - - -
102L LEU* 1.3 73.9 - - - +
104L HIS* 1.3 67.9 + - - +
106L LEU* 3.0 13.9 + - - +
107L SER 3.1 9.4 + - - -
144L PRO* 3.2 22.3 - - + +
145L VAL 3.7 2.0 + - - +
146L HIS* 3.1 49.7 + - - +
147L VAL* 3.4 13.6 + - + +
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Residues in contact with HIS 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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382H GLU* 5.3 7.8 + - - -
100L ASN 3.1 14.9 + - - +
101L GLU* 3.5 11.0 - - - +
103L ASN* 1.3 77.8 - - - +
105L CYS* 1.3 66.1 + - - +
107L SER* 2.8 35.1 + - - -
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Residues in contact with CYS 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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205J CYS* 4.9 10.3 - - + -
206J PRO* 5.5 9.0 - - - -
80L HIS* 5.6 1.3 - - - -
81L TRP* 3.6 37.9 - - + -
101L GLU* 3.0 35.7 + - - +
102L LEU 3.7 6.1 - - - +
103L ASN 3.2 0.2 - - - -
104L HIS* 1.3 81.4 - - - +
106L LEU* 1.3 58.4 + - - +
107L SER* 3.4 1.1 + - - -
108L LEU 4.9 0.5 + - - -
109L ARG* 3.0 41.4 + - - +
112L LEU* 4.9 2.2 - - + -
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Residues in contact with LEU 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 LEU* 3.2 29.1 + - + +
103L ASN 3.0 8.1 + - - +
105L CYS* 1.3 74.9 - - - +
107L SER* 1.3 55.4 - - - +
108L LEU 3.4 2.7 - - - -
109L ARG* 3.1 26.9 - - + +
111L TYR 4.6 0.4 - - - -
112L LEU* 3.8 27.4 - - + +
146L HIS* 3.6 11.4 - - + +
147L VAL* 4.1 12.3 - - - -
149L ARG* 2.7 32.5 + - - +
150L TRP* 3.7 56.5 - - + -
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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