Contacts of the strand formed by residues 118 - 127 (chain C) in PDB entry 4QAE
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 HIS 118 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C TRP* 3.6 7.4 - - - -
112C SER* 4.2 14.5 + - - -
113C THR* 2.5 29.2 + - - -
114C ASN* 3.0 58.1 + - + +
117C GLN* 1.3 84.8 + - - +
119C ALA* 1.3 65.5 + - - +
120C MET* 5.5 2.2 - - + -
137C LEU* 5.1 4.9 - - + -
138C TYR 3.2 11.4 - - - +
144C LEU* 3.9 19.1 - - + -
148C LEU* 3.9 28.8 - - + +
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Residues in contact with ALA 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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27C PHE* 3.6 23.1 - - + -
31C TRP* 3.9 2.7 - - + -
110C VAL* 5.2 0.2 - - + -
112C SER 3.2 11.2 - - - +
113C THR* 3.4 15.0 - - - +
118C HIS* 1.3 81.8 - - - +
120C MET* 1.3 71.5 + - - +
121C VAL* 4.6 0.2 - - + -
136C THR 4.3 0.2 - - - -
137C LEU* 3.5 3.3 - - - +
138C TYR* 2.8 42.9 + - + +
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Residues in contact with MET 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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110C VAL* 3.8 0.7 - - - -
111C VAL* 2.8 36.0 + - + -
112C SER* 2.8 20.3 + - - +
118C HIS* 5.5 3.1 - - + -
119C ALA* 1.3 78.8 - - - +
121C VAL* 1.3 63.6 + - - +
135C VAL* 3.7 6.5 - - + -
136C THR 3.1 5.8 - - - +
137C LEU* 3.7 15.3 - - + -
148C LEU 5.3 0.2 - - - +
151C ASN* 4.2 15.7 - - - +
152C PHE* 3.3 44.2 - - + -
155C PHE* 3.2 41.7 - - + -
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Residues in contact with VAL 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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27C PHE* 4.0 16.6 - - + -
56C TYR* 4.7 1.8 - - - +
108C VAL* 3.7 19.5 - - + -
109C ARG 3.5 14.8 - - - +
110C VAL* 4.2 8.5 - - + +
111C VAL* 4.3 1.1 - - - +
120C MET* 1.3 81.1 - - - +
122C PHE* 1.3 63.8 + - - +
123C PHE* 3.5 25.9 - - + -
135C VAL* 3.2 8.2 - - - -
136C THR* 2.9 39.9 + - - +
138C TYR* 3.6 29.6 - - + -
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Residues in contact with PHE 122 (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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11C PRO* 4.0 24.0 - - + -
13C LEU* 4.0 21.5 - - + -
16C VAL* 3.7 33.7 - - + -
107C LEU* 4.2 7.2 - - + -
108C VAL* 3.5 2.4 - - - -
109C ARG* 2.8 47.5 + - + +
111C VAL* 3.8 6.3 - - + +
121C VAL* 1.3 75.8 - - - +
123C PHE* 1.3 62.3 + - - +
124C LYS* 3.8 25.4 - - + -
133C PHE* 3.6 38.4 - + + -
134C TRP 3.6 3.4 - - - -
135C VAL* 4.1 20.2 - - + -
159C LEU* 4.4 2.9 - - + -
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Residues in contact with PHE 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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54C THR* 6.1 0.2 - - + -
56C TYR* 3.9 2.5 - - - -
81C GLN* 5.6 1.3 - - - -
83C PHE* 3.8 26.0 - + - -
94C LEU* 6.2 0.4 - - + -
107C LEU 3.4 4.0 - - - +
108C VAL* 3.8 24.9 - - + -
121C VAL* 3.5 24.0 - - + -
122C PHE* 1.3 78.0 - - - +
124C LYS* 1.3 59.8 + - - +
133C PHE* 3.1 7.4 - - - +
134C TRP* 2.8 79.5 + + + +
136C THR* 3.4 29.4 - - + -
138C TYR* 3.4 20.6 - - - -
9R PHE* 6.4 0.2 - + - -
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Residues in contact with LYS 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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10C ALA* 3.7 26.5 - - + -
11C PRO 5.8 0.9 - - - +
13C LEU* 4.3 16.7 - - - +
106C GLY* 3.4 0.5 - - - -
107C LEU* 2.9 58.7 + - + +
122C PHE* 3.8 18.1 - - + -
123C PHE* 1.3 75.8 - - - +
125C VAL* 1.3 80.3 + - - +
126C VAL* 5.5 4.8 - - - +
131C GLU* 2.9 27.9 + - + +
132C VAL 3.3 11.7 - - - +
133C PHE* 4.2 3.1 - - + -
134C TRP* 5.0 0.4 - - - -
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Residues in contact with VAL 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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94C LEU* 4.3 9.9 - - + -
105C SER 4.2 5.8 - - - +
106C GLY* 4.1 13.9 - - - -
124C LYS* 1.3 83.0 - - - +
126C VAL* 1.3 65.3 + - - +
131C GLU* 3.4 4.7 - - - -
132C VAL* 2.9 41.9 + - + +
134C TRP* 4.0 15.7 - - + -
8R ILE* 3.6 26.2 - - + -
9R PHE 4.5 2.0 - - - +
10R CYS* 4.0 6.7 - - - -
13R CYS* 3.6 30.5 - - - -
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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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105C SER* 3.9 28.2 + - - +
124C LYS* 5.5 4.7 - - - +
125C VAL* 1.3 80.1 - - - +
127C TRP* 1.3 61.4 + - - +
128C GLN 5.1 0.2 - - - +
129C ASN* 4.4 19.5 - - - +
130C ARG 3.3 10.3 - - - +
131C GLU* 4.7 15.9 - - + +
8R ILE* 4.5 4.0 - - - +
24R LYS* 3.2 24.3 + - - +
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Residues in contact with TRP 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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78A TYR* 4.9 0.2 - - - -
175A CYS 6.0 0.7 - - - -
177A ASP 5.9 4.7 - - - -
125C VAL* 3.8 2.1 + - + -
126C VAL* 1.3 74.3 - - - +
128C GLN* 1.3 99.0 + - + +
129C ASN 3.2 0.9 - - - -
130C ARG* 2.8 60.0 + - - +
132C VAL* 4.1 6.3 - - + -
8R ILE* 4.3 14.8 - - + -
13R CYS* 3.4 44.4 + - + -
14R CYS* 4.0 13.8 - - + +
22R CYS* 3.5 38.6 - - + -
23R CYS 3.3 26.0 - - - -
24R LYS* 3.8 27.8 - - + +
25R THR* 6.1 0.2 - - - -
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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