Contacts of the helix formed by residues 84 - 102 (chain C) in PDB entry 4XNW
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 84 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C PRO 3.7 3.8 + - - -
83C TRP* 1.3 76.1 - - - +
85C GLY* 1.3 66.0 + - - +
86C ILE* 3.0 17.5 + - - +
87C SER* 3.0 10.3 + - - -
88C VAL* 3.2 11.5 + - - +
148C HIS* 5.3 4.3 - - - -
163C LEU 5.7 0.7 - - - -
165C LYS* 4.8 2.7 - - - +
329C ASP* 2.3 37.8 + - - -
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Residues in contact with GLY 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C SER* 1.3 74.8 - - - +
86C ILE* 1.3 60.8 + - - +
88C VAL* 3.3 5.7 + - - +
89C TYR* 3.0 32.9 + - - -
148C HIS* 3.8 16.7 + - - -
163C LEU 4.2 9.0 + - - -
165C LYS* 4.5 5.1 - - - +
168C ALA* 3.3 25.1 - - - -
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Residues in contact with ILE 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C SER* 3.0 10.5 - - - +
85C GLY* 1.3 77.8 - - - +
87C SER* 1.3 52.3 + - - +
89C TYR* 3.1 6.8 + - - +
90C MET* 2.7 64.2 + - + +
145C ILE* 4.1 22.0 - - + +
148C HIS* 3.4 41.0 + - + +
149C ARG* 3.6 42.2 - - - +
327C ALA 4.7 0.2 - - - +
328C GLY* 4.2 4.7 - - - -
329C ASP* 4.2 6.1 - - - +
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Residues in contact with SER 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C PHE* 3.7 19.8 - - - -
80C MET* 3.4 27.3 - - - +
83C TRP* 3.9 26.2 - - - -
84C SER* 3.0 10.6 + - - -
86C ILE* 1.3 74.9 - - - +
88C VAL* 1.3 60.9 + - - +
90C MET* 4.4 2.0 - - - -
91C PHE* 2.8 32.3 + - - +
329C ASP* 3.7 14.2 + - - +
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Residues in contact with VAL 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C TRP* 4.1 22.2 - - + -
84C SER 3.2 13.1 + - - +
85C GLY 3.3 7.6 - - - +
86C ILE 3.1 0.4 - - - -
87C SER* 1.3 79.2 - - - +
89C TYR* 1.3 64.3 + - - +
91C PHE* 3.2 3.3 + - - +
92C ASN* 3.1 29.3 + - - +
165C LYS* 4.1 24.2 - - + -
168C ALA* 3.6 21.3 - - + +
169C ILE* 4.1 16.8 - - + +
172C SER* 3.4 21.5 - - - +
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Residues in contact with TYR 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C GLY 3.0 21.1 + - - -
86C ILE* 3.6 8.7 - - - +
88C VAL* 1.3 78.1 - - - +
90C MET* 1.3 62.3 + - - +
92C ASN* 2.9 18.2 + - - +
93C LEU* 3.1 10.4 + - - +
141C PHE* 4.0 20.5 - + + -
144C CYS* 3.7 37.1 - - + +
145C ILE* 3.6 22.7 - - + -
148C HIS* 3.7 24.0 - + + -
168C ALA* 3.6 29.6 - - - +
171C ILE* 3.3 42.6 - - + +
172C SER* 3.5 11.4 - - - -
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Residues in contact with MET 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C PHE* 3.8 19.5 - - + -
86C ILE* 2.7 34.0 + - + +
87C SER* 4.2 2.0 - - - +
89C TYR* 1.3 72.9 - - - +
91C PHE* 1.3 60.7 + - - +
93C LEU* 3.2 9.2 + - + +
94C ALA* 3.0 23.6 + - - +
145C ILE* 4.0 29.2 - - + -
323C LEU* 3.9 18.2 - - + +
324C TYR* 3.8 28.0 - - + +
327C ALA* 3.9 12.6 - - + +
328C GLY* 3.5 39.7 - - - +
329C ASP 5.1 0.2 - - - -
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Residues in contact with PHE 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ILE* 4.2 31.0 - - + -
76C PHE* 4.0 27.5 - + + -
77C VAL* 4.8 7.6 - - + -
83C TRP* 3.6 36.3 - + + -
87C SER 2.8 24.5 + - - +
88C VAL 3.5 4.5 - - - +
90C MET* 1.3 73.0 - - - +
92C ASN* 1.3 65.2 + - - +
94C ALA* 3.3 2.8 + - + +
95C LEU* 2.9 58.2 + - + +
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Residues in contact with ASN 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C VAL* 3.1 23.4 + - - +
89C TYR 2.9 8.8 + - - +
91C PHE* 1.3 82.7 - - - +
93C LEU* 1.3 56.1 + - - +
95C LEU* 3.4 15.9 - - - +
96C ALA* 3.0 28.8 + - - +
141C PHE* 3.4 22.8 - - + -
172C SER* 3.2 32.7 + - - -
176C TRP* 2.9 31.7 + - - +
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Residues in contact with LEU 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C TYR 3.1 7.7 + - - +
90C MET* 3.2 7.6 + - - +
92C ASN* 1.3 73.7 - - - +
94C ALA* 1.3 65.9 + - - +
96C ALA* 3.0 6.1 + - + +
97C ASP* 2.9 27.5 + - - +
138C SER* 3.5 43.5 - - - +
141C PHE* 4.0 15.0 - - + -
142C LEU* 3.7 29.2 - - + -
145C ILE* 3.9 19.7 - - + -
320C ASN* 4.2 13.9 - - - +
323C LEU* 4.5 4.9 - - + -
324C TYR* 3.3 23.6 - - + +
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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
----------------------------------------------------------
69C ASN* 3.8 11.0 - - - +
72C ALA* 4.3 8.3 - - + -
73C ILE* 3.9 20.6 - - + +
76C PHE* 4.7 3.1 - - + -
90C MET 3.0 10.7 + - - +
91C PHE* 3.6 10.3 - - - +
93C LEU* 1.3 74.4 - - - +
95C LEU* 1.3 61.9 + - - +
97C ASP 3.6 0.2 + - - -
98C PHE* 3.0 26.7 + - - +
324C TYR* 3.0 32.6 + - + -
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Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ILE* 4.3 17.4 - - + +
91C PHE* 2.9 47.2 + - + +
92C ASN* 3.4 19.3 - - - +
93C LEU 3.1 0.2 - - - -
94C ALA* 1.3 78.2 - - - +
96C ALA* 1.3 61.9 + - - +
98C PHE* 3.4 3.3 + - + +
99C LEU* 3.2 43.8 + - + +
176C TRP* 5.2 7.6 - - + +
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Residues in contact with ALA 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ASN 3.0 12.2 + - - +
93C LEU* 3.8 5.8 - - + +
95C LEU* 1.3 73.9 - - - +
97C ASP* 1.3 60.9 + - - +
99C LEU* 4.0 7.0 - - - +
100C TYR* 3.1 23.0 + - - +
130C ILE* 5.8 0.2 - - - +
133C VAL* 6.3 0.2 - - + -
134C ASN* 3.2 27.9 + - - +
137C GLY* 6.0 0.4 - - - -
138C SER* 5.3 6.5 - - - +
141C PHE* 6.0 1.6 - - + -
176C TRP* 3.4 31.8 - - + -
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Residues in contact with ASP 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ASN* 3.8 20.9 - - - +
93C LEU* 2.9 16.1 + - - +
94C ALA 4.0 0.2 - - - +
96C ALA* 1.3 75.3 - - - +
98C PHE* 1.3 58.0 - - - +
100C TYR* 3.5 1.7 + - - +
101C VAL* 3.0 35.3 + - - +
134C ASN* 3.1 16.9 + - - +
138C SER* 4.1 6.1 + - - -
316C ASN* 4.5 2.1 - - - +
317C SER* 2.8 31.6 + - - +
320C ASN* 3.0 30.1 + - - +
324C TYR* 3.3 15.9 + - - -
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Residues in contact with PHE 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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65C GLY 5.5 0.2 - - - -
66C PHE* 3.5 35.9 - + - -
69C ASN* 4.2 8.9 - - + +
70C SER* 3.2 36.6 - - - -
73C ILE* 3.8 19.7 - - + -
94C ALA 3.0 18.0 + - - +
95C LEU* 3.7 5.4 - - + +
96C ALA 3.3 0.2 - - - -
97C ASP* 1.3 74.7 - - - +
99C LEU* 1.3 79.9 + - + +
101C VAL* 3.2 17.3 + - + +
102C LEU* 3.3 35.5 + - + +
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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
----------------------------------------------------------
95C LEU* 3.2 34.1 + - + +
96C ALA* 4.1 6.3 - - - +
98C PHE* 1.3 92.6 - - + +
100C TYR* 1.3 64.3 + - - +
102C LEU* 3.3 26.5 + - + +
103C THR* 3.8 9.0 + - - +
130C ILE* 4.5 9.3 - - + +
176C TRP* 6.2 1.8 - - + -
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Residues in contact with TYR 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C TYR* 4.8 1.4 + - - -
96C ALA 3.1 18.8 + - - +
97C ASP 3.7 2.9 - - - +
99C LEU* 1.3 74.1 - - - +
101C VAL* 1.3 57.8 + - - +
103C THR* 2.5 51.2 + - - -
104C LEU* 3.8 22.8 + - + +
107C LEU* 5.0 5.2 - - + +
127C GLN* 5.7 2.5 - - - -
130C ILE* 4.0 12.7 - - + +
131C PHE* 3.5 48.6 - + + -
134C ASN* 3.8 23.1 - - + -
314C SER* 2.7 39.0 + - - -
317C SER* 3.4 25.1 - - - -
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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
----------------------------------------------------------
61C VAL 4.8 1.1 - - - +
62C PHE* 3.4 46.6 - - + +
65C GLY* 4.1 19.7 - - - +
66C PHE* 3.8 14.6 - - + +
69C ASN* 4.8 0.2 - - - +
97C ASP 3.0 26.1 + - - +
98C PHE* 3.2 10.3 + - + +
100C TYR* 1.3 76.0 - - + +
102C LEU* 1.3 57.2 + - - +
104C LEU* 2.9 39.9 + - + +
317C SER* 4.0 20.4 - - - -
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Residues in contact with LEU 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C PHE* 4.7 5.2 - - + -
66C PHE* 3.9 33.9 - - + -
98C PHE* 3.3 32.9 + - + +
99C LEU* 3.4 22.9 - - + +
100C TYR 3.0 0.4 + - - -
101C VAL* 1.3 80.4 - - + +
103C THR* 1.3 56.2 + - + +
104C LEU 3.3 0.9 - - - -
105C PRO* 3.4 18.0 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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