Contacts of the helix formed by residues 88 - 101 (chain C) in PDB entry 5W4A
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 88 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C VAL* 3.9 36.8 - - + -
60C ILE* 4.0 38.1 - - + -
61C VAL* 4.4 4.3 - - + -
81C LEU* 3.6 45.8 - - + +
84C LEU* 3.4 42.2 - - + -
85C GLY 3.0 3.1 + - - +
87C ASP* 1.3 92.8 - - + +
89C LEU* 1.3 60.0 + - - +
90C THR 3.4 2.9 - - - -
91C GLU* 3.3 11.0 + - + +
92C PHE* 3.0 25.6 + - - +
178C ILE* 5.5 3.4 - - + -
179C LEU* 5.7 1.8 - - + -
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Residues in contact with LEU 89 (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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81C LEU 5.6 0.9 - - - -
82C LEU* 4.1 26.2 - - + -
85C GLY 3.6 7.2 + - - +
86C PRO* 3.3 18.6 + - + +
88C PHE* 1.3 76.2 - - - +
90C THR* 1.3 65.2 + - - +
92C PHE* 3.3 13.0 + - + +
93C LYS* 3.0 37.6 + - + +
111C LEU* 6.2 2.2 - - + -
112C ALA* 5.3 8.7 - - + +
116C GLU* 5.3 8.5 - - - +
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Residues in contact with THR 90 (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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86C PRO 4.7 2.1 + - - -
87C ASP 5.3 1.9 - - - -
88C PHE 3.4 0.4 - - - -
89C LEU* 1.3 78.9 - - - +
91C GLU* 1.3 62.3 + - - +
93C LYS* 3.2 10.1 + - + +
94C LYS* 3.0 25.7 + - + +
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Residues in contact with GLU 91 (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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57C VAL* 6.2 1.6 - - + -
61C VAL* 3.7 30.9 - - + +
65C PHE* 4.8 0.2 - - + -
81C LEU* 3.8 18.4 - - + -
87C ASP 5.7 0.4 + - - +
88C PHE* 3.3 14.3 + - + +
89C LEU 3.3 0.2 - - - -
90C THR* 1.3 79.0 - - - +
92C PHE* 1.3 62.6 + - - +
94C LYS* 3.3 29.7 + - - +
95C ARG* 2.8 65.9 + - - +
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Residues in contact with PHE 92 (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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78C MSE 3.5 43.4 - - + +
81C LEU* 3.6 14.2 - - + +
82C LEU* 3.5 37.9 - - + -
88C PHE 3.0 13.7 + - - +
89C LEU* 3.5 17.3 - - + +
90C THR 3.2 0.2 - - - -
91C GLU* 1.3 76.1 - - - +
93C LYS* 1.3 67.0 + - + +
95C ARG* 3.3 2.4 + - - +
96C ASN* 2.9 35.5 + - - +
106C HIS* 3.7 34.8 - + + -
108C LEU 5.1 5.2 - - - -
109C SER* 5.1 2.5 - - - -
111C LEU* 6.2 0.4 - - + -
112C ALA* 4.2 19.3 - - + -
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Residues in contact with LYS 93 (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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89C LEU* 3.0 30.9 + - + +
90C THR* 3.2 11.4 + - + +
92C PHE* 1.3 80.8 - - + +
94C LYS* 1.3 57.4 + - - +
96C ASN* 3.3 5.2 + - - +
97C GLN* 2.9 30.1 + - - +
112C ALA* 3.7 46.1 + - + +
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Residues in contact with LYS 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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90C THR* 3.0 16.5 + - + +
91C GLU* 3.6 35.9 + - - +
93C LYS* 1.3 77.2 - - - +
95C ARG* 1.3 70.1 + - - +
97C GLN* 3.3 11.5 + - - +
98C ASP* 3.1 27.5 + - - +
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Residues in contact with ARG 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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61C VAL* 3.9 9.5 - - - +
62C GLN* 6.0 1.2 - - - +
65C PHE* 3.5 62.5 + - + +
69C SER* 6.2 0.4 - - - -
74C ILE* 4.5 13.4 - - + +
78C MSE 3.8 21.8 - - + -
81C LEU* 4.6 0.2 - - + -
91C GLU* 2.8 46.1 + - - +
92C PHE 3.8 3.6 - - - +
94C LYS* 1.3 83.2 - - - +
96C ASN* 1.3 63.0 + - - +
98C ASP* 3.3 15.8 + - - +
99C LEU* 3.2 24.9 + - - +
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Residues in contact with ASN 96 (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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78C MSE 3.4 16.4 - - + +
92C PHE* 2.9 26.0 + - + +
93C LYS* 3.7 7.9 - - - +
94C LYS 3.2 0.2 - - - -
95C ARG* 1.3 74.3 - - - +
97C GLN* 1.3 65.4 + - - +
99C LEU* 3.1 15.4 + - - +
100C ALA* 3.5 10.0 + - - +
104C LEU 4.6 1.2 - - - +
105C THR* 3.3 13.3 + - - -
106C HIS* 2.9 25.7 + - - -
109C SER* 2.8 28.6 + - - +
112C ALA* 5.4 3.0 - - - +
113C GLN* 4.1 10.3 - - - +
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Residues in contact with GLN 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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93C LYS 2.9 17.0 + - - +
94C LYS* 3.6 9.2 - - - +
96C ASN* 1.3 75.3 - - - +
98C ASP* 1.3 64.3 + - - +
100C ALA* 3.2 20.6 + - - +
101C ARG* 4.3 6.1 + - - +
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Residues in contact with ASP 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 LYS* 3.1 17.1 + - - +
95C ARG* 3.4 20.9 + - - +
97C GLN* 1.3 78.1 + - - +
99C LEU* 1.3 63.6 + - + +
100C ALA 3.4 0.5 + - - -
101C ARG* 3.7 30.6 + - - +
102C PHE* 3.5 20.9 - - + -
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Residues in contact with LEU 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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71C SER* 5.2 6.5 - - - +
74C ILE* 4.1 27.6 - - + -
75C LEU* 3.7 29.8 - - + -
78C MSE 3.7 19.7 - - - -
95C ARG 3.2 11.5 + - - +
96C ASN* 3.1 16.8 + - - +
98C ASP* 1.3 80.5 - - + +
100C ALA* 1.3 64.5 + - - +
102C PHE* 2.9 23.2 + - + +
104C LEU* 3.2 46.6 + - + +
105C THR* 4.3 6.3 - - - +
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Residues in contact with ALA 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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96C ASN 3.5 7.2 + - - +
97C GLN* 3.2 15.7 + - + +
99C LEU* 1.3 79.2 - - - +
101C ARG* 1.3 58.5 + - + +
103C ASN* 2.9 23.4 + - - +
104C LEU 3.6 10.3 - - - +
105C THR* 6.3 0.4 - - - -
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Residues in contact with ARG 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 GLN 4.5 6.5 - - - +
98C ASP* 3.7 33.2 + - - +
99C LEU 3.2 0.6 + - - -
100C ALA* 1.3 77.1 - - + +
102C PHE* 1.3 98.9 + - + +
103C ASN* 3.3 5.7 + - - +
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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