Contacts of the helix formed by residues 96 - 105 (chain C) in PDB entry 2YIN
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 LYS 96 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ASP* 5.4 0.7 - - - +
60C GLY 4.2 6.9 + - - -
61C GLN 4.2 6.1 + - - -
62C GLU* 4.0 21.6 - - - +
65C ASP* 3.2 29.6 + - - -
68C ARG* 3.9 12.5 - - - +
92C ASN* 2.7 33.6 + - + +
95C ALA* 1.3 76.4 - - - +
97C TRP* 1.3 88.1 + - + +
98C TYR 3.7 1.1 - - - -
99C PRO* 3.6 4.6 - - - +
100C GLU* 3.2 25.2 + - + +
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Residues in contact with TRP 97 (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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9C VAL* 4.1 15.0 - - + -
10C GLY* 3.3 46.8 - - - -
11C ASP* 2.9 27.0 + - - +
58C THR* 5.8 0.2 - - - -
60C GLY* 3.8 28.0 - - - -
68C ARG* 3.7 33.4 - - - -
80C ILE* 4.2 20.6 - - + -
81C CYS 4.9 5.4 - - - -
89C SER 4.9 1.1 - - - -
92C ASN* 2.9 34.0 + - + +
93C VAL* 4.0 9.4 - - + +
96C LYS* 1.3 89.2 - - + +
98C TYR* 1.3 69.3 + - - +
100C GLU* 2.9 22.5 + - - +
101C VAL* 3.0 15.0 + - + +
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Residues in contact with TYR 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ILE* 4.2 14.6 - - + +
93C VAL* 2.9 19.5 + - + +
94C ARG* 5.1 3.6 - - + -
97C TRP* 1.3 73.5 - - - +
99C PRO* 1.3 75.8 - - + +
101C VAL* 3.2 1.1 + - - +
102C ARG* 2.5 71.0 + - + +
110C ILE* 4.0 13.0 - - + -
148C GLU* 4.9 3.0 + - + -
149C ILE* 3.2 56.1 + - + -
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Residues in contact with PRO 99 (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 VAL 3.8 1.1 - - - +
94C ARG 3.3 25.1 - - - +
95C ALA 3.8 12.8 - - - +
96C LYS 3.6 7.6 - - - +
97C TRP 3.6 2.2 - - - -
98C TYR* 1.3 100.4 - - + +
100C GLU* 1.3 62.4 + - - +
102C ARG* 4.2 3.7 - - + +
103C HIS* 2.9 28.2 + - - +
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Residues in contact with GLU 100 (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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65C ASP* 4.3 7.4 - - - +
68C ARG* 2.7 35.4 + - - -
69C PRO* 4.1 14.1 - - + +
72C TYR* 2.9 27.3 + - + -
96C LYS* 3.2 14.7 + - + +
97C TRP* 2.9 18.5 + - - +
99C PRO* 1.3 79.6 - - - +
101C VAL* 1.3 64.3 + - - +
103C HIS* 3.6 3.1 - - - +
104C HIS* 3.1 44.0 + - + +
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Residues in contact with VAL 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C VAL* 4.4 11.4 - - + -
72C TYR* 4.6 15.0 - - + +
78C PHE* 3.7 48.9 - - + -
80C ILE* 4.3 14.1 - - + -
97C TRP* 3.0 14.2 + - + +
98C TYR 3.7 6.3 - - - +
100C GLU* 1.3 75.9 - - + +
102C ARG* 1.3 57.0 + - - +
104C HIS* 2.9 4.2 + - - +
105C CYS* 2.6 39.6 + - - +
108C THR 5.4 0.2 - - - +
110C ILE* 3.9 22.9 - - + -
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Residues in contact with ARG 102 (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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98C TYR* 2.5 56.9 + - + +
99C PRO* 4.2 3.8 - - + +
101C VAL* 1.3 78.9 - - - +
103C HIS* 1.3 62.2 + - - +
105C CYS 3.7 5.1 + - - -
106C PRO* 2.8 59.5 + - + +
107C ASN 4.0 1.4 - - - -
108C THR 2.7 30.4 + - - +
109C PRO* 5.1 1.6 - - - +
110C ILE* 3.7 21.1 - - - +
149C ILE 4.4 2.8 + - - -
150C GLY* 3.5 22.8 + - - -
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Residues in contact with HIS 103 (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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99C PRO 2.9 20.8 + - - +
100C GLU* 3.6 5.4 - - - +
101C VAL 3.1 0.2 - - - -
102C ARG* 1.3 78.5 - - - +
104C HIS* 1.3 90.6 + + + +
106C PRO* 4.7 5.2 - - - +
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Residues in contact with HIS 104 (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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69C PRO* 3.4 37.4 + - + +
72C TYR* 3.8 21.3 - + + +
100C GLU* 3.1 33.6 + - + +
101C VAL 2.9 3.4 + - - +
103C HIS* 1.3 105.2 - + - +
105C CYS* 1.3 66.1 + - - +
106C PRO* 3.7 6.3 - - - +
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Residues in contact with CYS 105 (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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72C TYR* 3.3 37.5 - - - -
73C PRO* 4.7 6.7 - - - -
75C THR* 5.1 0.4 - - - -
78C PHE* 3.8 22.9 - - + -
101C VAL* 2.6 19.7 + - - +
102C ARG* 3.5 15.8 + - - -
104C HIS* 1.3 81.2 - - - +
106C PRO* 1.3 70.0 - - - +
107C ASN 3.3 3.4 + - - -
108C THR* 3.5 22.8 + - - +
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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