Contacts of the strand formed by residues 118 - 128 (chain C) in PDB entry 6PAI
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 118 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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907A ASN* 3.1 18.3 + - - -
944A GLU* 5.4 1.5 + - - -
68C ILE* 3.4 10.2 - - - +
115C ASN* 2.8 38.3 + - - +
116C VAL 3.6 4.7 - - - +
117C HIS* 1.3 82.5 - - - +
119C LYS* 1.3 66.8 + - - +
120C LEU* 3.8 1.4 + - - +
121C LYS* 5.4 3.5 - - - -
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Residues in contact with LYS 119 (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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66C LYS 5.3 1.3 - - - -
67C ASN* 3.2 26.1 + - - +
68C ILE 3.2 9.9 - - - +
69C VAL 3.5 23.8 - - - +
70C ASP* 3.9 20.0 - - - +
71C GLU* 5.9 6.7 - - + +
113C GLU 4.4 2.1 - - - +
115C ASN* 5.1 2.1 - - - +
117C HIS 5.3 0.2 - - - +
118C SER* 1.3 83.3 + - - +
120C LEU* 1.3 63.9 + - - +
121C LYS* 3.4 15.0 + - - +
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Residues in contact with LEU 120 (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 LEU* 4.6 2.5 - - + -
68C ILE* 2.6 49.1 + - + +
69C VAL* 4.0 12.1 - - + -
70C ASP* 3.6 18.2 + - - +
80C PHE* 3.8 29.6 - - + -
90C VAL* 4.6 8.7 - - + -
112C TRP* 3.6 31.6 - - + -
113C GLU 3.6 4.5 - - - +
114C PHE* 3.6 35.9 - - + +
115C ASN 4.7 1.6 - - - +
116C VAL 6.0 0.2 - - - +
118C SER 5.2 0.7 - - - +
119C LYS* 1.3 70.4 - - - +
121C LYS* 1.3 63.2 + - - +
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Residues in contact with LYS 121 (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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990A GLN* 4.2 24.2 + - - +
70C ASP* 5.6 0.7 - - - -
112C TRP* 3.2 6.8 - - - -
113C GLU* 2.8 59.4 + - + +
115C ASN* 4.3 24.9 - - - +
118C SER* 5.4 3.4 - - - -
119C LYS 3.4 10.7 + - - +
120C LEU* 1.3 74.6 - - - +
122C LEU* 1.3 63.2 + - - +
123C VAL* 3.8 2.2 - - + +
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Residues in contact with LEU 122 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C ASP* 5.5 1.0 + - - +
73C PHE* 4.2 25.1 - - + -
110C TYR* 3.9 23.8 - - + -
111C TRP 3.8 5.6 - - - +
112C TRP* 3.5 44.8 - - + -
120C LEU 3.9 0.6 + - - -
121C LYS* 1.3 74.1 - - - +
123C VAL* 1.3 61.7 + - - +
124C ARG 4.1 7.2 - - - +
125C GLN* 4.3 22.7 - - + +
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Residues in contact with VAL 123 (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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987A GLU* 6.5 1.1 - - - -
89C TYR* 4.3 13.9 - - + +
111C TRP* 2.9 14.4 + - + +
113C GLU* 3.7 37.9 - - + +
121C LYS* 3.8 4.3 - - + +
122C LEU* 1.3 77.9 - - - +
124C ARG* 1.3 63.9 + - + +
188C PRO* 4.2 22.0 - - + -
208C ASN* 5.1 6.6 - - - +
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Residues in contact with ARG 124 (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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109C LEU 4.5 0.2 - - - -
110C TYR* 3.1 8.9 - - - +
111C TRP* 2.9 49.2 + - + +
122C LEU* 3.9 5.2 - - - +
123C VAL* 1.3 82.2 + - - +
125C GLN* 1.3 62.8 + - - +
126C VAL* 3.6 27.1 - - + -
185C VAL* 5.0 1.1 - - - +
186C ALA* 3.1 28.2 + - - +
187C VAL 3.5 0.6 - - - -
188C PRO* 3.4 37.6 - - + +
189C PRO* 3.6 9.9 - - - +
210C GLN* 3.6 22.8 + - - +
214C HIS 2.9 29.6 + - - -
215C GLY* 4.5 3.6 - - - -
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Residues in contact with GLN 125 (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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73C PHE* 6.0 0.5 - - - -
108C HIS* 4.6 16.2 + - + -
109C LEU 3.4 4.3 - - - -
110C TYR* 3.3 37.1 + - + -
122C LEU* 4.3 16.4 - - + +
124C ARG* 1.3 76.1 - - - +
126C VAL* 1.3 70.6 + - - +
208C ASN* 5.8 2.8 + - - +
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Residues in contact with VAL 126 (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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108C HIS* 3.0 6.3 - - - -
109C LEU* 2.6 44.6 + - + +
111C TRP* 4.7 1.1 - - + -
124C ARG* 3.6 28.5 - - + -
125C GLN* 1.3 86.9 - - - +
127C ARG* 1.3 73.8 + - - +
128C LEU* 4.8 2.5 - - + -
185C VAL* 3.9 34.5 - - + -
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Residues in contact with ARG 127 (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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106C ILE* 3.4 31.8 - - + +
107C TYR 3.3 10.5 - - - +
108C HIS* 3.5 27.9 + - + +
126C VAL* 1.3 85.3 - - - +
128C LEU* 1.3 73.7 + - - +
129C PHE 4.3 0.4 + - - -
130C GLN* 4.5 32.5 - - + +
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Residues in contact with LEU 128 (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 TYR* 5.0 2.9 - - + -
107C TYR* 2.5 39.9 + - + +
108C HIS 4.2 2.5 - - - +
109C LEU* 3.9 33.2 - - + +
126C VAL* 4.6 1.1 - - + +
127C ARG* 1.3 86.9 - - - +
129C PHE* 1.3 90.7 + - + +
130C GLN 3.5 1.1 + - - -
140C LEU* 4.1 19.7 - - + -
154C VAL* 4.2 21.5 - - + -
183C SER* 4.4 8.3 - - - -
185C VAL* 4.1 24.5 - - + -
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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