Contacts of the helix formed by residues 106 - 114 (chain C) in PDB entry 4Y1L
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 106 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68C TYR* 3.0 24.4 + - + +
69C PRO* 4.0 10.8 - - + +
71C CYS 4.8 1.8 - - - +
73C PRO* 4.0 19.1 - - + -
98C ALA* 3.2 39.3 - - - +
101C LEU* 3.3 47.3 - - + +
102C LEU* 3.8 9.2 - - + -
104C GLU 3.0 9.1 + - - +
105C PRO* 1.3 74.0 - - - +
107C VAL* 1.3 68.3 + - + +
108C HIS 3.4 2.7 - - - -
109C GLU* 3.0 13.0 + - - +
110C LEU* 2.9 32.7 + - + +
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Residues in contact with VAL 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLU* 3.1 16.4 + - - +
19C LEU* 3.6 23.6 - - + -
42C PHE* 3.7 26.9 - - + -
62C PHE* 4.0 24.9 - - + -
64C LEU* 4.3 9.2 - - + -
68C TYR* 3.3 22.7 - - + +
73C PRO* 5.7 1.1 - - + -
106C MET* 1.3 78.9 - - + +
108C HIS* 1.3 65.3 + - - +
110C LEU* 3.1 8.7 + - - +
111C VAL* 2.9 31.7 + - + +
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Residues in contact with HIS 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B SER* 4.3 6.3 + - - -
10B ALA* 3.4 33.4 + - + +
11B GLN* 4.1 17.9 - - - -
14B LYS* 4.2 24.1 + - - +
15C GLU* 3.9 3.0 + - - +
18C VAL* 5.8 0.7 - - + -
19C LEU* 3.8 20.3 - - + +
22C ILE* 3.3 26.9 - - + +
23C PHE* 6.0 0.7 - + - -
105C PRO 5.9 0.2 - - - +
106C MET 3.4 0.4 - - - -
107C VAL* 1.3 77.8 - - - +
109C GLU* 1.3 71.6 + - + +
111C VAL* 3.4 6.9 + - + +
112C LEU* 3.0 48.3 + - + +
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Residues in contact with GLU 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLN* 5.4 5.1 - - - +
14B LYS* 4.3 17.4 - - + +
101C LEU* 3.5 33.3 - - + +
105C PRO 4.4 6.3 - - - +
106C MET* 3.0 17.0 + - - +
108C HIS* 1.3 88.4 + - + +
110C LEU* 1.3 56.4 + - - +
112C LEU* 3.7 3.2 - - - +
113C TRP* 2.8 30.9 + - - +
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Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C LEU* 6.6 0.4 - - - -
62C PHE* 4.2 27.6 - - + -
73C PRO* 5.3 1.3 - - + -
75C ILE* 4.8 4.7 - - + -
94C LEU* 3.9 34.8 - - + +
97C GLN* 4.3 6.1 - - + +
98C ALA* 3.9 26.9 - - + +
101C LEU* 3.8 22.0 - - + -
106C MET* 2.9 30.8 + - + +
107C VAL* 3.1 5.1 + - - +
109C GLU* 1.3 72.1 - - - +
111C VAL* 1.3 60.8 + - - +
113C TRP* 2.8 30.8 + - + +
114C ILE* 3.0 14.8 + - - +
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Residues in contact with VAL 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU* 5.1 0.9 - - + -
23C PHE* 3.9 27.6 - - + -
44C ILE* 4.6 11.7 - - + -
46C THR* 3.9 28.0 - - + +
60C LEU* 5.4 6.1 - - + -
62C PHE* 4.3 14.3 - - + -
107C VAL* 2.9 36.1 + - + +
108C HIS* 3.5 10.1 - - + +
110C LEU* 1.3 80.0 - - - +
112C LEU* 1.3 59.8 + - + +
113C TRP 3.2 0.2 + - - -
114C ILE* 3.2 17.2 + - - +
115C GLN* 2.7 20.1 - - - +
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Residues in contact with LEU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B SER* 3.9 23.3 - - - +
11B GLN* 4.4 10.3 - - - +
22C ILE* 6.5 0.9 - - + -
46C THR* 5.6 2.0 - - - +
108C HIS* 3.0 40.8 + - + +
109C GLU* 3.7 3.1 - - - +
111C VAL* 1.3 78.1 - - + +
113C TRP* 1.3 58.6 + - - +
115C GLN* 2.4 56.0 + - + +
116C GLU* 3.1 15.4 - - - +
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Residues in contact with TRP 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C LYS* 4.1 26.9 - - + -
94C LEU* 3.4 33.9 - - + -
97C GLN* 3.2 33.2 + - + +
109C GLU 2.8 18.4 + - - +
110C LEU* 2.8 17.5 + - + +
112C LEU* 1.3 78.6 - - - +
114C ILE* 1.3 74.7 - - + +
115C GLN 3.7 0.2 - - - -
116C GLU* 3.5 14.5 - - - +
117C ASN* 3.1 48.1 + - + +
119C ARG* 5.5 3.1 - - - -
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Residues in contact with ILE 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C THR* 4.9 5.2 - - + -
48C ALA* 4.1 6.9 - - - +
58C LEU* 3.8 28.1 - - + +
60C LEU* 5.0 4.7 - - + -
90C VAL* 3.9 18.2 - - + -
93C LYS* 5.1 3.4 - - - +
94C LEU* 3.6 38.8 - - + -
110C LEU 3.0 8.5 + - - +
111C VAL* 3.5 14.8 - - - +
112C LEU 3.2 0.2 - - - -
113C TRP* 1.3 94.8 - - + +
115C GLN* 1.3 57.0 + - - +
116C GLU 3.1 4.0 - - - -
117C ASN 2.5 35.3 - - - +
118C LEU* 4.2 7.3 - - + +
119C ARG 5.5 0.9 - - - +
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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