Contacts of the strand formed by residues 106 - 113 (chain C) in PDB entry 1F15
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 ARG 106 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62C GLU* 3.9 18.9 + - - +
63C ARG 3.3 21.0 + - - -
64C CYS* 4.1 1.2 - - - +
65C ARG* 3.0 41.9 - - - +
104C VAL* 4.2 3.6 - - - +
105C SER* 1.3 83.9 + - - +
107C LEU* 1.3 67.7 + - - +
167C LEU* 3.4 39.7 - - + +
168C TYR 3.6 12.6 - - - +
169C ASP* 3.9 19.7 - - + +
170C LEU 4.0 1.1 - - - +
205C ILE 4.1 0.2 - - - -
206C GLU* 2.6 74.4 + - + +
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Residues in contact with LEU 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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90C LEU* 3.7 24.2 - - + -
104C VAL* 4.8 1.1 - - + -
106C ARG* 1.3 79.4 - - - +
108C GLN* 1.3 60.2 + - - +
109C ILE* 3.9 3.8 + - - +
125C VAL* 4.0 24.0 - - + -
168C TYR* 3.1 31.0 + - + +
170C LEU* 3.2 31.6 - - + -
180C MET* 3.2 29.2 - - + -
183C TYR* 4.7 8.1 - - + -
203C VAL* 4.6 7.2 - - + -
204C ASP 3.5 10.5 - - - +
205C ILE* 4.5 7.9 - - + -
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Residues in contact with GLN 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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53B ILE* 4.1 3.8 - - - +
61C SER* 2.6 30.1 + - - -
62C GLU* 5.8 0.2 - - - +
106C ARG 4.1 0.2 - - - -
107C LEU* 1.3 72.4 - - - +
109C ILE* 1.3 73.5 + - - +
110C ARG* 3.3 18.4 + - - -
165C LYS* 3.4 20.9 - - + +
166C LEU 3.4 10.5 - - - +
167C LEU* 3.4 29.4 - - + +
203C VAL* 3.6 3.1 - - - +
204C ASP* 2.8 60.2 + - + +
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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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107C LEU 4.4 2.0 - - - +
108C GLN* 1.3 87.6 - - - +
110C ARG* 1.3 69.9 + - - +
111C VAL* 4.8 1.6 - - + -
123C VAL* 4.0 22.2 - - + -
125C VAL* 3.3 44.6 - - + -
165C LYS* 4.7 0.2 - - - -
166C LEU* 3.1 40.4 + - + -
185C VAL* 3.9 9.9 - - + -
201C LEU* 4.1 13.0 - - + -
202C HIS 3.4 6.5 - - - +
203C VAL* 3.8 30.1 - - + -
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Residues in contact with ARG 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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70C PHE* 6.0 0.4 - - - -
72C SER* 4.1 9.3 + - - -
108C GLN* 3.3 16.0 + - - +
109C ILE* 1.3 80.3 - - - +
111C VAL* 1.3 63.0 - - - +
112C ASN* 3.7 15.2 + - - +
164C ASN* 3.4 14.6 - - - +
165C LYS* 4.0 20.2 - - + +
201C LEU* 3.4 2.9 - - - -
202C HIS* 2.9 81.6 + - + +
204C ASP* 2.8 31.6 + - - +
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Residues in contact with VAL 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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109C ILE* 4.8 1.8 - - + -
110C ARG* 1.3 75.1 - - - +
112C ASN* 1.3 61.6 + - - +
113C PRO* 3.9 3.1 - - - +
123C VAL* 4.2 22.0 - - + -
151C LEU* 4.8 9.4 - - + -
153C TYR* 4.2 23.6 - - + -
164C ASN* 3.0 34.7 + - - +
199C LEU* 3.3 39.5 - - + -
200C VAL 4.1 2.9 - - - -
201C LEU* 3.7 26.2 - - + +
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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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58C PHE* 4.0 14.7 - - + -
110C ARG* 3.7 20.9 + - - +
111C VAL* 1.3 75.9 - - - +
113C PRO* 1.3 71.5 - - + +
114C LEU* 5.2 2.0 - - + +
164C ASN* 3.7 13.4 + - - +
199C LEU* 3.8 1.9 - - - +
200C VAL* 3.1 36.1 + - + +
202C HIS* 3.4 33.9 + - + -
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Residues in contact with PRO 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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58C PHE* 3.5 15.1 - - + -
111C VAL 3.9 0.2 - - - +
112C ASN* 1.3 89.2 - - - +
114C LEU* 1.3 65.0 + - - +
115C PRO* 4.6 1.7 - - - +
117C PHE* 3.7 32.8 - - + -
153C TYR* 3.2 37.2 - - + +
160C VAL* 3.6 21.8 - - + -
198C GLU 3.6 4.9 - - - +
199C LEU* 4.5 2.9 - - + -
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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