Contacts of the strand formed by residues 104 - 113 (chain C) in PDB entry 1LNU
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 ASN 104 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94C PRO* 4.1 5.1 - - - +
95C LYS* 3.4 10.2 + - - +
96C SER* 2.5 42.6 + - - -
97C PRO 3.2 17.4 + - - -
98C VAL* 4.2 4.0 - - - +
99C LEU 5.1 0.6 - - - +
102C GLN 3.4 6.0 + - - +
103C PRO* 1.3 75.5 + - - +
105C THR* 1.3 92.2 + - - +
153C THR* 3.9 3.4 - - - +
154C PHE* 2.8 53.9 + - + +
156C PRO* 4.8 4.3 - - + -
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Residues in contact with THR 105 (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 PRO* 3.4 0.9 - - - +
95C LYS* 2.6 56.7 + - - +
104C ASN* 1.3 90.8 + - - +
106C LEU* 1.3 60.7 + - - +
107C ILE* 3.7 0.9 + - + +
151C TYR* 3.7 35.7 - - + -
152C LEU 3.2 17.0 - - - +
153C THR* 4.2 11.6 + - - +
154C PHE* 4.0 1.8 - - - -
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Residues in contact with LEU 106 (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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92C VAL* 3.5 27.6 - - + -
93C PHE 4.0 10.1 - - - -
94C PRO* 4.1 3.1 - - + -
105C THR* 1.3 72.7 - - - +
107C ILE* 1.3 60.3 + - - +
122C TRP* 3.2 36.4 - - + -
151C TYR* 3.5 2.6 - - - -
152C LEU* 2.8 49.2 + - + +
154C PHE* 3.8 12.5 - - + -
162C TYR* 4.2 24.9 - - + -
179C TRP* 3.7 36.3 - - + -
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Residues in contact with ILE 107 (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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91C THR 3.5 0.9 - - - +
92C VAL* 2.9 6.8 - - - +
93C PHE* 2.7 82.1 + - + +
95C LYS* 4.2 17.0 - - + -
105C THR 4.1 7.2 - - - +
106C LEU* 1.3 75.7 - - - +
108C CYS* 1.3 63.5 + - - +
122C TRP* 4.1 2.0 - - - -
149C LEU* 3.9 21.5 - - + -
150C SER 3.5 6.5 - - - +
151C TYR* 3.6 23.1 - - + -
177D ASN* 3.8 33.2 - - + +
179D ASP* 5.4 0.2 - - - +
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Residues in contact with CYS 108 (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 ALA* 4.8 11.9 - - - -
91C THR 3.4 3.1 - - - -
92C VAL* 3.5 11.2 - - - -
107C ILE* 1.3 73.0 - - - +
109C PHE* 1.3 63.3 + - - +
110C VAL* 3.7 10.8 + - - +
120C ILE* 4.7 2.0 - - + -
122C TRP* 3.4 19.3 - - + -
148C LYS 3.8 0.5 - - - +
149C LEU* 3.7 2.4 - - - -
150C SER* 3.0 36.0 + - - +
164C CYS* 2.0 50.7 - - - -
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Residues in contact with PHE 109 (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 GLN* 5.6 4.0 - - + -
90C ALA* 3.3 4.0 + - - -
91C THR* 2.6 55.0 + - + +
93C PHE* 3.7 18.2 - + + -
107C ILE* 3.9 1.0 - - - +
108C CYS* 1.3 72.1 - - - +
110C VAL* 1.3 60.7 + - - +
111C ASP* 3.8 33.4 + - + -
147C HIS* 3.5 32.8 - + + -
149C LEU* 3.3 30.1 - - + -
176D ARG 5.9 1.8 - - - -
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Residues in contact with VAL 110 (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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88C PRO* 3.8 21.1 - - + -
89C GLN 3.0 23.3 - - - +
90C ALA* 5.2 0.7 - - - -
108C CYS* 4.0 9.9 - - - +
109C PHE* 1.3 78.3 - - - +
111C ASP* 1.3 60.3 + - - +
113C ILE* 3.8 17.5 - - + -
118C ILE* 3.8 8.7 - - + -
120C ILE* 3.5 30.7 - - + -
147C HIS* 2.8 27.1 - - - +
148C LYS 2.9 16.6 + - - +
166C VAL* 4.2 15.9 - - + -
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Residues in contact with ASP 111 (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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88C PRO* 3.4 2.4 - - - +
89C GLN* 3.0 43.1 + - - +
109C PHE* 3.8 25.4 + - + -
110C VAL* 1.3 76.4 - - - +
112C ASN* 1.3 83.6 + - - +
113C ILE 3.3 2.9 + - - -
141C ASN* 2.4 35.9 + - - +
147C HIS* 3.0 12.9 - - - +
137F ASN 5.6 2.1 - - - +
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Residues in contact with ASN 112 (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 GLU* 4.1 24.7 + - - +
87C ALA 3.2 24.1 + - - +
88C PRO* 3.5 12.8 - - - +
89C GLN* 4.3 14.8 - - + +
111C ASP* 1.3 92.7 + - + +
113C ILE* 1.3 61.5 + - - +
114C PHE* 3.8 1.8 + - - -
141C ASN* 4.2 0.4 + - - +
143C ASP* 4.0 5.0 - - - +
145C SER* 3.7 20.6 + - - -
146C PHE 2.9 3.6 + - - -
60D ARG* 3.9 12.0 + - - -
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Residues in contact with ILE 113 (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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88C PRO* 4.3 4.3 - - + -
110C VAL* 3.8 31.6 - - + +
112C ASN* 1.3 73.1 - - - +
114C PHE* 1.3 68.4 + - - +
115C PRO 3.6 7.2 - - - +
116C PRO* 4.4 0.7 - - + -
118C ILE* 4.1 19.1 - - + -
138C PHE* 4.3 16.8 - - + -
145C SER* 3.7 0.5 - - - -
146C PHE* 2.6 46.5 + - + +
147C HIS* 3.7 4.3 - - - +
148C LYS* 3.4 40.2 - - + +
168C HIS* 3.3 24.7 - - + +
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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