Contacts of the strand formed by residues 103 - 112 (chain C) in PDB entry 1I3R
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 103 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93C SER* 4.6 0.7 - - - -
94C ARG* 3.8 2.4 + - - +
95C SER* 3.1 37.6 + - - -
96C PRO 3.0 28.9 + - - -
97C VAL* 3.7 12.1 - - - +
98C ASN 4.8 1.0 - - - +
101C GLU* 4.1 7.3 + - - +
102C PRO* 1.3 76.0 + - - +
104C ILE* 1.3 90.0 + - - +
152C THR* 3.8 2.8 - - - +
153C PHE* 3.0 48.3 + - + +
155C PRO* 4.2 2.5 - - + -
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Residues in contact with ILE 104 (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 SER* 3.5 2.8 - - - -
94C ARG* 2.8 66.6 + - + +
103C ASN* 1.3 92.5 + - - +
105C LEU* 1.3 73.8 + - - +
106C ILE* 4.4 0.2 - - + -
150C TYR* 4.0 25.1 - - + -
151C LEU 3.6 6.1 - - - +
152C THR* 4.4 17.9 - - + +
153C PHE* 3.4 4.0 - - - -
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Residues in contact with LEU 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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91C VAL* 4.3 5.6 - - + -
92C LEU 3.8 13.9 - - - +
93C SER* 4.4 1.1 - - - -
104C ILE* 1.3 74.3 - - - +
106C ILE* 1.3 58.5 + - - +
121C TRP* 3.6 25.0 - - + -
150C TYR* 3.5 6.6 - - - -
151C LEU* 2.8 41.2 + - + +
153C PHE* 3.5 22.8 - - + -
161C TYR* 3.4 50.0 - - + -
178C TRP* 3.8 35.0 - - + -
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Residues in contact with ILE 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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90C THR 3.4 1.2 - - - +
91C VAL* 3.1 6.2 - - - +
92C LEU* 2.6 58.8 + - + +
93C SER 4.5 0.2 - - - -
94C ARG* 3.7 25.6 - - + +
104C ILE* 4.3 0.4 - - + +
105C LEU* 1.3 75.9 - - - +
107C CYS* 1.3 61.4 + - - +
108C PHE* 4.2 4.3 - - + +
121C TRP* 4.0 2.2 - - - -
148C PHE* 3.9 27.8 - - + -
149C HIS 3.6 5.4 - - - +
150C TYR* 4.0 14.6 - - + -
175D ARG 5.7 0.2 - - - +
176D ASN* 3.1 47.8 - - + +
182D GLN* 4.5 2.2 - - - +
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Residues in contact with CYS 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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89C VAL* 3.8 21.5 - - - -
90C THR 3.4 2.7 - - - -
91C VAL* 4.2 3.1 - - - +
106C ILE* 1.3 75.1 - - - +
108C PHE* 1.3 57.6 + - - +
109C ILE* 3.5 14.4 + - - +
121C TRP* 3.4 19.9 - - + -
147C LYS 3.7 0.3 - - - +
148C PHE* 3.7 1.9 - - - -
149C HIS* 2.8 36.8 + - + +
163C CYS* 2.0 49.8 - - + -
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Residues in contact with PHE 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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88C GLU 3.6 2.1 - - - +
89C VAL* 3.4 4.6 - - - -
90C THR* 2.6 52.3 + - - +
92C LEU* 4.9 5.8 - - + -
106C ILE* 3.8 5.7 + - + -
107C CYS* 1.3 69.8 - - - +
109C ILE* 1.3 62.5 + - - +
110C ASP* 3.4 37.1 + - + -
146C ARG* 3.9 30.1 - - + -
147C LYS 3.9 3.8 - - - -
148C PHE* 3.5 44.6 - + + -
175D ARG 5.9 0.2 - - - -
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Residues in contact with ILE 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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87C PRO* 3.7 23.6 - - + -
88C GLU 3.6 4.5 - - - +
89C VAL* 4.7 2.0 - - + +
107C CYS* 3.8 14.4 - - - +
108C PHE* 1.3 72.2 - - - +
110C ASP* 1.3 60.2 + - - +
112C PHE* 3.5 21.6 - - + -
117C VAL* 4.8 5.8 - - + -
119C VAL* 3.3 35.9 - - + -
146C ARG* 3.2 4.7 - - - +
147C LYS* 2.7 47.1 + - + +
149C HIS* 4.1 13.0 - - + +
165C VAL* 3.7 27.4 - - + -
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Residues in contact with ASP 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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87C PRO* 3.2 4.2 - - - +
88C GLU* 2.9 42.1 + - + +
108C PHE* 3.4 34.9 - - + -
109C ILE* 1.3 74.3 - - - +
111C LYS* 1.3 102.8 + - + +
112C PHE* 3.6 4.3 - - - -
140C ARG* 2.7 32.3 + - - -
145C PHE 4.1 1.6 - - - -
146C ARG* 3.4 8.0 - - - +
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Residues in contact with LYS 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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61B GLU* 4.2 23.2 + - - -
85C VAL* 3.6 10.4 - - + +
86C ALA 3.2 17.5 - - - +
88C GLU* 3.3 35.1 + - + +
110C ASP* 1.3 102.7 + - - +
112C PHE* 1.3 57.7 + - - +
140C ARG* 3.4 31.9 - - - +
144C LEU* 4.0 24.4 - - + +
145C PHE 3.2 7.2 + - - -
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Residues in contact with PHE 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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85C VAL 3.2 14.4 - - - +
87C PRO* 3.4 31.6 - - + -
109C ILE* 3.5 27.6 - - + -
110C ASP 3.8 5.2 - - - -
111C LYS* 1.3 74.3 - - - +
113C SER* 1.3 65.1 + - - +
114C PRO 3.7 15.5 - - - -
115C PRO* 4.3 1.6 - - + -
117C VAL* 3.8 15.7 - - + -
137C PHE* 3.7 37.9 - + - -
144C LEU* 3.7 6.6 - - - +
145C PHE* 3.0 52.6 + - + -
146C ARG* 3.7 0.9 - - - -
147C LYS* 4.0 12.6 - - + -
167C HIS* 3.8 9.0 - + + -
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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
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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