Contacts of the strand formed by residues 104 - 112 (chain C) in PDB entry 3IN7
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 ASP 104 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C AYQ 5.6 1.6 + - - -
75C SER* 5.8 0.6 - - - -
100C LYS* 3.7 5.0 - - - +
101C PHE* 3.0 32.3 + - + +
103C ASN* 1.3 81.0 - - - +
105C VAL* 1.3 94.0 + - - +
106C GLN* 4.1 13.6 - - + +
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Residues in contact with VAL 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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71C GLU* 3.8 39.8 - - + +
74C LEU* 4.0 27.1 - - + -
75C SER* 3.9 22.2 - - - +
98C SER* 4.3 1.1 - - - -
99C VAL 3.3 11.2 - - - +
100C LYS* 4.6 2.7 - - - -
104C ASP* 1.3 93.4 + - - +
106C GLN* 1.3 64.6 + - - +
107C HIS* 3.8 32.4 + - + -
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Residues in contact with GLN 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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1C AYQ 3.7 31.0 + - + +
97C LEU 3.8 0.7 - - - +
98C SER* 3.3 4.2 - - - -
99C VAL* 2.8 40.1 + - + +
101C PHE* 3.8 19.8 - - + -
104C ASP* 4.5 14.0 - - + +
105C VAL* 1.3 75.6 - - - +
107C HIS* 1.3 60.5 + - - +
108C PHE* 3.6 24.9 - - + -
141C SER* 4.6 3.0 + - - -
144C GLN* 3.7 21.9 + - - +
146C ILE* 3.4 24.9 - - - +
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Residues in contact with HIS 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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1C AYQ 2.8 50.9 + - + +
67C ARG* 3.5 53.9 - - + +
70C ALA* 4.8 0.4 - - + -
71C GLU* 2.9 41.4 + - + +
86C ARG* 3.1 10.5 + - - +
97C LEU 3.4 2.2 - - - -
98C SER* 2.8 33.4 + - - -
105C VAL* 3.8 16.3 + - + -
106C GLN* 1.3 74.1 - - - +
108C PHE* 1.3 58.7 + - - +
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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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1C AYQ 3.3 53.6 - - + +
96C SER* 3.5 4.3 - - - -
97C LEU* 2.7 60.2 + - + +
99C VAL* 3.9 26.7 - - + -
106C GLN* 3.6 31.4 - - + -
107C HIS* 1.3 76.7 - - - +
109C LYS* 1.3 59.9 + - - +
120C LEU* 4.3 8.5 - - + -
121C TRP* 4.0 9.2 - + - -
140C VAL* 3.2 40.4 - - + -
141C SER* 4.3 5.2 - - - -
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Residues in contact with LYS 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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1C AYQ 2.8 77.2 + - + +
88C SER* 4.6 2.0 + - - -
90C SER* 4.9 1.2 + - - -
91C ALA* 3.4 31.6 - - - +
94C ASP* 4.6 10.2 + - + +
95C PHE 4.4 5.1 + - - +
96C SER* 4.8 0.6 + - - +
108C PHE* 1.3 72.9 - - - +
110C VAL* 1.3 68.5 + - - +
111C LEU* 3.4 31.0 + - + +
119C PHE 4.0 0.2 - - - +
120C LEU* 3.7 3.8 - - - +
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Residues in contact with VAL 110 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C ILE* 4.2 15.5 - - + -
94C ASP* 4.5 10.0 - - - +
95C PHE* 3.1 45.9 + - + +
96C SER 4.2 0.2 - - - +
97C LEU* 4.1 19.7 - - + +
109C LYS* 1.3 74.4 - - - +
111C LEU* 1.3 62.0 + - - +
112C ARG* 4.1 1.4 + - - +
118C TYR* 3.8 29.5 - - + -
119C PHE 3.9 2.2 - - - +
120C LEU* 4.3 8.1 - - + -
128C LEU* 3.9 12.1 - - + -
131C LEU* 4.0 20.4 - - + -
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Residues in contact with LEU 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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1C AYQ 4.6 14.6 - - - +
109C LYS* 3.9 37.9 - - + +
110C VAL* 1.3 74.9 - - - +
112C ARG* 1.3 60.6 + - - +
118C TYR* 3.3 5.0 - - - +
119C PHE* 2.8 68.2 + - + +
120C LEU 4.2 15.9 - - - +
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Residues in contact with ARG 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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92A PRO 4.8 0.6 + - - -
93A GLY* 3.0 35.9 + - - -
94A ASP* 3.5 15.6 + - - -
112A ARG* 3.6 30.7 - - - +
94C ASP* 5.3 9.3 + - - +
110C VAL 4.1 1.7 + - - +
111C LEU* 1.3 76.1 - - - +
113C ASP* 1.3 63.6 + - - +
116C GLY* 3.0 40.7 + - - +
117C LYS 3.3 8.3 - - - +
118C TYR* 3.8 21.9 - - + -
119C PHE* 4.0 3.9 - - - -
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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