Contacts of the helix formed by residues 93 - 107 (chain C) in PDB entry 4H7Y
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 PHE 93 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C GLY 4.1 4.0 - - - -
56C GLN 3.5 23.6 - - - -
57C ASN 3.8 17.3 - - - -
58C GLU* 3.6 36.6 - - + -
61C ALA* 3.6 17.0 - - + -
90C CYS* 3.3 8.4 + - + -
91C LYS 3.2 2.0 - - - -
92C LYS* 1.3 108.8 - - + +
94C ALA* 1.3 65.6 + - - +
95C PHE* 3.7 29.4 - + + -
96C VAL* 3.0 17.4 + - + +
97C HIS* 3.2 15.4 - - - -
125C ALA* 4.2 0.2 - - - -
126C VAL* 3.7 9.2 - - + -
127C PRO* 6.3 0.2 - - + -
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Residues in contact with ALA 94 (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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92C LYS 3.6 1.8 + - - -
93C PHE* 1.3 71.6 - - - +
95C PHE* 1.3 58.6 + - - +
97C HIS* 3.1 6.3 + - - +
98C ILE* 2.9 30.5 + - - +
125C ALA* 4.0 9.6 - - - -
126C VAL 2.8 33.2 + - - +
127C PRO 3.6 14.6 - - - +
130C MET* 4.2 12.1 - - + -
131C LEU* 3.7 21.0 - - + +
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Residues in contact with PHE 95 (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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58C GLU* 4.4 11.7 - - + -
61C ALA* 3.6 25.1 - - + -
62C ARG* 3.7 25.1 - - + -
65C VAL* 3.8 29.6 - - + -
93C PHE* 3.1 34.3 + + + -
94C ALA* 1.3 79.0 - - - +
96C VAL* 1.3 59.0 + - + +
98C ILE* 3.9 5.9 - - - +
99C SER* 2.9 29.6 + - - -
126C VAL 5.9 0.2 - - - -
127C PRO* 5.7 0.2 - - - +
130C MET* 3.8 25.2 - - + +
146C LEU* 5.7 2.9 - - + -
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Residues in contact with VAL 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ALA* 4.0 8.7 - - + -
65C VAL* 3.6 28.4 - - + +
83C PHE* 5.4 0.9 - - - +
86C ALA* 3.6 34.5 - - + +
87C ARG* 3.7 11.9 - - + +
90C CYS* 3.7 28.5 - - + +
93C PHE* 3.3 19.7 - - + +
95C PHE* 1.3 82.3 - - + +
97C HIS* 1.3 62.8 + - + +
99C SER* 3.4 4.5 + - - -
100C PHE* 3.3 20.8 + - + +
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Residues in contact with HIS 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ARG* 3.5 39.1 + - + +
91C LYS* 2.7 34.6 + - + -
93C PHE 3.2 25.8 - - - -
94C ALA 3.1 5.1 + - - +
96C VAL* 1.3 77.0 - - + +
98C ILE* 1.3 61.3 + - - +
100C PHE* 3.3 8.1 + - - +
101C ALA* 2.9 28.3 + - - +
116C LEU* 4.6 13.2 + - + +
117C LEU* 4.6 1.5 - - + +
119C LYS* 5.8 0.7 - - + -
120C ALA* 3.5 35.8 + - + +
123C ARG* 5.8 5.6 - - + -
125C ALA* 3.7 13.8 - - + +
131C LEU* 4.6 2.0 - - + -
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Residues in contact with ILE 98 (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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94C ALA 2.9 19.0 + - - +
95C PHE* 3.9 5.8 - - - +
96C VAL 3.3 0.2 - - - -
97C HIS* 1.3 74.3 - - - +
99C SER* 1.3 55.4 + - - +
101C ALA* 3.6 1.0 - - - +
102C GLN* 2.7 35.8 + - + +
117C LEU* 3.8 14.8 - - + -
130C MET* 3.4 53.6 - - + +
131C LEU* 3.8 15.9 - - + +
134C ALA* 3.9 6.5 - - + -
145C LEU* 4.1 24.5 - - + -
146C LEU* 4.1 18.4 - - + -
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Residues in contact with SER 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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65C VAL* 3.3 23.0 - - - +
69C GLU* 2.8 24.9 + - - +
83C PHE* 3.5 23.1 - - - -
95C PHE 2.9 19.5 + - - -
96C VAL 3.6 6.1 - - - -
98C ILE* 1.3 76.6 - - - +
100C PHE* 1.3 57.1 + - - +
102C GLN* 3.3 8.4 + - - +
103C PHE 3.0 21.8 + - - -
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Residues in contact with PHE 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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80C ARG* 4.2 9.6 - - + -
83C PHE* 3.5 42.1 - + + +
84C GLN* 3.5 44.0 - - + -
87C ARG* 3.8 27.8 - - + -
96C VAL 3.3 10.3 + - - +
97C HIS* 3.5 9.9 - - - +
98C ILE 3.2 0.4 - - - -
99C SER* 1.3 76.4 - - - +
101C ALA* 1.3 64.2 + - - +
103C PHE* 3.1 7.2 + + - +
104C GLU* 3.0 47.5 + - + +
112C LYS* 5.7 3.8 - - - -
116C LEU* 3.7 21.1 - - + -
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Residues in contact with ALA 101 (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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97C HIS 2.9 17.2 + - - +
98C ILE 3.6 3.6 - - - +
100C PHE* 1.3 76.4 - - - +
102C GLN* 1.3 56.9 + - - +
104C GLU 3.4 0.6 + - - +
105C LEU* 2.9 19.1 + - - +
113C SER* 2.7 48.1 + - - +
116C LEU* 3.7 14.2 - - + +
117C LEU* 3.6 19.1 - - + -
145C LEU* 3.7 4.5 - - + -
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Residues in contact with GLN 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 ILE* 2.7 22.5 + - + +
99C SER* 3.5 9.2 - - - +
100C PHE 3.2 0.2 - - - -
101C ALA* 1.3 69.8 - - - +
103C PHE* 1.3 66.9 + - - +
105C LEU* 3.5 5.5 - - - +
106C SER* 3.0 33.1 + - - -
143C LYS 3.0 22.4 + - - -
144C GLN* 3.5 24.0 + - - +
145C LEU* 2.8 42.4 + - + +
146C LEU 4.6 0.7 + - - -
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Residues in contact with PHE 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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72C ALA* 3.8 22.9 - - + -
76C PRO* 3.3 28.9 - - + -
79C ALA* 4.1 1.3 - - + -
80C ARG* 4.0 51.6 - - + -
83C PHE* 3.5 40.2 - + + -
99C SER 3.0 7.7 + - - +
100C PHE* 3.1 11.0 + + - +
102C GLN* 1.3 77.8 - - - +
104C GLU* 1.3 74.0 + - + +
106C SER* 3.0 21.4 + - - -
107C GLN* 3.2 34.4 + - + +
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Residues in contact with GLU 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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80C ARG* 2.6 36.4 + - - -
100C PHE* 3.0 34.1 + - + +
101C ALA 3.8 4.0 - - - +
103C PHE* 1.3 79.9 - - - +
105C LEU* 1.3 60.2 + - - +
107C GLN* 3.2 7.2 + - - +
109C ASN* 2.8 69.7 + - + +
112C LYS* 3.9 16.9 - - + +
113C SER* 4.0 8.7 - - - +
116C LEU* 3.8 17.3 - - + -
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Residues in contact with LEU 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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101C ALA 2.9 17.9 + - - +
102C GLN* 3.5 7.6 - - - +
104C GLU* 1.3 77.7 - - - +
106C SER* 1.3 55.4 + - - +
108C GLY* 2.8 25.1 + - - -
109C ASN 4.2 2.2 - - - +
110C VAL* 4.1 19.7 - - + -
113C SER* 3.7 9.8 - - - +
138C LEU* 3.7 21.5 - - + -
142C LYS 3.7 16.6 - - - +
143C LYS* 3.6 25.8 - - - +
145C LEU* 3.9 27.4 - - + -
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Residues in contact with SER 106 (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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102C GLN* 3.0 24.4 + - - +
103C PHE* 3.0 18.7 + - - -
105C LEU* 1.3 78.2 - - - +
107C GLN* 1.3 73.2 + - - +
108C GLY 3.2 1.3 + - - -
143C LYS 6.0 0.4 - - - -
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Residues in contact with GLN 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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76C PRO* 3.5 39.8 - - - +
77C ASP* 4.0 9.7 - - - +
80C ARG* 4.9 2.5 - - - +
103C PHE* 3.2 36.3 + - + +
104C GLU 3.6 8.3 - - - +
105C LEU 3.1 1.0 - - - -
106C SER* 1.3 94.9 + - - +
108C GLY* 1.3 60.0 + - - +
109C ASN* 3.6 19.2 + - - +
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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