Contacts of the strand formed by residues 131 - 143 (chain C) in PDB entry 6H25
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 LEU 131 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C PHE* 4.6 20.6 - - + -
67C ALA* 3.5 14.8 - - - +
69C PRO* 4.3 0.9 - - - +
126C ILE* 3.4 17.9 + - + -
127C SER* 3.1 27.9 + - - +
130C LYS* 1.3 88.1 - - + +
132C VAL* 1.3 64.1 + - - +
170C ILE* 3.8 29.2 - - + -
175C ALA* 3.8 22.7 - - + -
20F TYR* 6.5 0.7 - - + -
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Residues in contact with VAL 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C PHE* 3.7 1.7 - - - -
67C ALA* 2.9 42.8 + - + +
68C ALA 4.3 0.4 - - - -
69C PRO* 3.8 31.6 - - + -
74C PRO 5.8 0.2 - - - +
75C ASP* 4.4 2.5 - - - +
76C LYS 3.3 22.9 - - - +
77C GLY* 3.7 11.9 - - - -
78C TYR* 5.1 4.3 - - + +
124C LEU 3.3 21.3 - - - +
125C CYS* 3.7 13.0 - - + -
126C ILE* 4.2 9.5 - - - +
127C SER 5.6 0.2 - - - +
131C LEU* 1.3 75.7 - - - +
133C TRP* 1.3 66.0 + - - +
134C VAL* 5.2 3.6 - - + -
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Residues in contact with TRP 133 (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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64C ALA* 3.6 36.1 - - + -
65C GLU 3.9 9.4 - - - -
66C PHE* 3.9 30.5 - + - +
77C GLY* 4.0 3.5 - - - -
78C TYR 3.5 18.0 + - - +
123C ASP 5.6 0.4 - - - -
124C LEU* 3.3 43.2 + - + +
125C CYS 5.1 0.9 - - - -
126C ILE* 3.5 23.7 - - + +
132C VAL* 1.3 82.4 - - - +
134C VAL* 1.3 66.1 + - - +
135C LEU* 4.3 3.6 - - + -
165C LEU* 3.9 27.0 - - + +
166C PRO* 3.8 43.7 + - + -
168C VAL* 4.0 10.7 - - + +
17F PRO* 5.4 6.5 - - + -
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Residues in contact with VAL 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C LYS 3.6 1.0 - - - +
64C ALA* 3.3 5.2 - - - -
65C GLU* 2.9 39.9 + - + +
67C ALA* 3.7 27.8 - - + -
78C TYR* 3.6 26.2 - - + +
80C VAL* 5.0 1.1 - - + -
132C VAL* 4.4 3.1 - - + +
133C TRP* 1.3 79.4 - - - +
135C LEU* 1.3 64.9 + - - +
136C TYR* 3.6 40.7 + - + -
11F PRO* 3.8 14.1 - - + -
14F SER* 5.6 1.1 - - - -
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Residues in contact with LEU 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C VAL* 4.0 19.5 - - + -
63C LYS 3.4 11.4 - - - +
64C ALA* 3.9 19.1 - - + -
78C TYR 3.3 9.0 + - - +
79C VAL* 3.4 19.0 - - + +
80C VAL 2.9 26.7 + - - +
119C ILE* 5.8 4.5 - - + -
124C LEU* 4.5 18.6 - - + -
133C TRP* 5.4 2.7 - - + -
134C VAL* 1.3 74.4 - - - +
136C TYR* 1.3 63.3 + - - +
137C CYS* 3.7 4.0 + - - -
160C LEU* 5.4 9.9 - - + -
163C VAL* 4.8 7.6 - - + -
165C LEU* 4.7 13.0 - - + -
187C LEU* 3.8 28.0 - - + -
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Residues in contact with TYR 136 (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 GLY 3.4 1.7 - - - +
62C VAL* 3.2 4.5 - - - -
63C LYS* 2.9 43.0 + - + +
65C GLU* 4.9 9.4 - - + -
80C VAL* 3.6 33.2 - - + -
134C VAL* 3.6 24.8 + - + -
135C LEU* 1.3 70.9 - - - +
137C CYS* 1.3 61.3 + - - +
138C ASP* 3.8 2.9 + - - +
10F GLY* 5.7 0.2 - - - -
11F PRO* 3.3 25.5 + - + +
14F SER* 4.0 23.1 + - - -
110F ARG* 3.2 59.2 - - + +
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Residues in contact with CYS 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C CYS* 4.9 0.9 - - - -
61C GLY 3.4 4.9 - - - +
62C VAL* 3.7 26.7 - - + -
79C VAL* 4.4 20.9 - - - -
80C VAL 2.9 12.8 + - - +
81C PRO* 3.2 8.0 - - + +
82C ASN 2.9 26.0 + - - -
113C ILE* 5.5 1.1 - - - -
135C LEU* 4.4 3.8 - - - -
136C TYR* 1.3 72.9 - - - +
138C ASP* 1.3 61.0 + - - +
139C LEU* 3.6 8.2 - - + +
156C LEU* 4.0 19.1 - - + -
160C LEU* 3.8 19.3 - - - -
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Residues in contact with ASP 138 (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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59C ILE 3.9 1.0 - - - +
60C CYS* 3.6 1.6 - - - -
61C GLY* 2.9 34.9 + - - +
63C LYS* 5.7 0.9 - - - +
80C VAL 5.3 0.5 - - - +
82C ASN* 3.4 27.6 + - - +
136C TYR* 3.8 1.9 + - - +
137C CYS* 1.3 76.5 + - - +
139C LEU* 1.3 61.4 + - - +
140C ILE* 4.1 2.4 + - + -
104F PRO* 3.3 33.8 - - + +
105F PHE* 4.2 12.6 - - + +
110F ARG* 3.1 39.5 + - - -
113F PRO* 5.6 1.1 - - - -
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Residues in contact with LEU 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C VAL* 4.4 7.2 - - + -
59C ILE 3.4 5.2 - - - +
60C CYS* 3.6 32.8 - - + -
81C PRO* 5.2 0.2 - - + -
82C ASN 2.9 10.3 + - - +
83C VAL* 3.5 25.8 - - + +
84C ASP* 2.9 29.4 + - - +
109C ILE* 5.0 7.4 - - + -
137C CYS* 3.6 19.7 - - + +
138C ASP* 1.3 76.3 - - - +
140C ILE* 1.3 61.9 + - - +
141C CYS 3.9 0.8 + - - -
152C CYS* 3.4 49.1 - - + +
156C LEU* 4.5 7.2 - - + +
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Residues in contact with ILE 140 (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 VAL* 3.9 2.2 - - - -
59C ILE* 3.1 36.2 + - + +
84C ASP* 3.9 14.1 - - + +
86C PRO* 4.1 14.8 - - + -
138C ASP* 4.1 1.1 + - + -
139C LEU* 1.3 74.8 - - - +
141C CYS* 1.3 74.7 + - - +
142C LEU* 3.7 5.5 + - + +
103F ALA* 3.9 17.3 - - + -
104F PRO* 3.8 31.0 - - + -
105F PHE* 4.5 10.3 - - + -
149F LEU* 3.8 31.4 - - + -
151F LEU* 5.0 4.0 - - + -
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Residues in contact with CYS 141 (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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56C THR* 6.4 0.2 - - - -
57C THR 3.8 9.0 - - - -
58C VAL* 4.4 4.4 - - + +
83C VAL* 5.8 1.5 - - + +
84C ASP 3.6 7.9 + - - +
85C LEU* 3.7 25.1 - - + -
86C PRO* 3.8 14.8 - - + +
88C LEU* 4.8 0.9 - - - +
89C CYS* 4.2 6.7 - - + +
139C LEU 3.9 1.2 + - - -
140C ILE* 1.3 86.0 - - - +
142C LEU* 1.3 65.0 + - - +
143C ASP 3.8 26.0 - - - -
144C TYR* 3.9 14.4 - - - -
148C ILE* 3.8 26.0 - - + -
152C CYS* 6.3 0.4 - - - -
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Residues in contact with LEU 142 (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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50C LEU* 5.0 1.1 - - + -
57C THR* 2.8 39.8 + - + +
59C ILE* 3.7 31.4 - - + -
88C LEU* 3.7 29.9 - - + +
89C CYS* 3.3 21.3 + - - -
140C ILE* 4.4 8.7 - - + +
141C CYS* 1.3 78.8 - - - +
143C ASP* 1.3 60.1 + - - +
45F LEU* 6.3 1.6 - - + -
46F LEU* 3.9 18.1 - - + +
63F LEU* 4.2 23.1 - - + -
149F LEU* 4.2 13.5 - - + -
151F LEU* 5.1 4.5 - - + -
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Residues in contact with ASP 143 (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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55C ASN* 3.7 15.3 - - - +
56C THR* 3.3 26.0 - - - -
57C THR* 3.3 14.1 + - - +
89C CYS* 4.0 4.0 - - - +
141C CYS* 3.8 4.9 - - - -
142C LEU* 1.3 80.0 - - - +
144C TYR* 1.3 62.1 + - - +
145C ASP 3.6 0.2 + - - -
45F LEU 5.0 0.2 - - - +
46F LEU* 3.5 17.8 - - + +
47F SER* 2.6 42.5 + - - -
48F GLN* 3.2 27.5 + - - +
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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