Contacts of the strand formed by residues 103 - 113 (chain A) 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 LEU 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A TYR* 3.5 16.2 - - - +
101A LYS 4.3 8.5 - - - +
102A LYS* 1.3 72.1 - - - +
104A VAL* 1.3 56.3 + - - +
171A SER 6.0 1.1 - - - +
174A ARG* 4.0 54.1 - - + +
175A ALA 3.1 16.2 - - - +
176A ASP* 4.5 3.6 - - + +
207A HIS* 2.8 12.5 - - - +
208A GLN* 2.5 64.8 + - - +
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Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A TYR* 5.1 0.4 - - - -
102A LYS 3.6 0.2 + - - -
103A LEU* 1.3 75.5 - - - +
105A SER* 1.3 73.2 + - - +
107A LEU* 4.4 4.3 - - + -
170A LEU* 4.0 16.4 - - + +
171A SER* 4.1 11.8 + - - +
174A ARG* 5.4 0.2 - - - -
175A ALA* 2.8 23.2 + - + +
176A ASP 3.7 8.7 - - - -
177A ILE* 3.5 22.4 - - + -
180A MET* 3.5 43.5 - - + -
205A ILE* 3.9 11.2 - - + -
206A GLU 3.4 8.3 - - - +
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Residues in contact with SER 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ARG* 3.0 32.6 + - - -
68A TYR* 4.4 10.3 - - - -
103A LEU 4.2 0.2 - - - -
104A VAL* 1.3 78.0 - - - +
106A ARG* 1.3 71.8 + - - -
107A LEU* 4.7 0.2 - - - +
169A ASP* 3.0 18.2 + - - -
170A LEU* 3.1 26.5 + - - +
171A SER* 3.6 7.5 - - - +
206A GLU* 2.9 27.8 + - - -
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Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A GLU* 4.2 8.7 + - - +
63A ARG 3.5 7.1 + - - -
64A CYS* 2.9 22.6 - - - +
65A ARG* 3.5 12.9 - - - +
70A PHE* 3.8 8.0 - - + -
105A SER* 1.3 84.5 + - - +
107A LEU* 1.3 66.3 + - - +
167A LEU* 4.2 15.3 - - + -
168A TYR 3.3 15.9 - - - +
169A ASP* 3.8 19.5 + - + +
205A ILE* 4.9 0.5 - - - +
206A GLU* 2.9 63.8 + - + +
216B LEU* 3.6 35.3 - - + +
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Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A PHE* 5.2 1.6 - - - -
104A VAL* 4.4 6.7 - - + -
106A ARG* 1.3 78.6 - - - +
108A GLN* 1.4 60.5 + - - +
125A VAL* 4.0 21.5 - - + -
167A LEU* 3.3 26.3 - - - +
168A TYR* 3.0 33.6 + - + +
170A LEU* 4.3 24.0 - - + -
180A MET* 3.5 30.3 - - + -
183A TYR* 5.4 3.6 - - + -
203A VAL* 4.4 13.9 - - + -
204A ASP 3.2 15.0 - - - +
205A ILE* 4.2 6.3 - - + -
216B LEU* 6.0 0.4 - - - -
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Residues in contact with GLN 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A LEU* 1.4 74.0 - - - +
109A ILE* 1.4 60.3 + - - +
110A ARG* 3.1 10.3 - - + +
125A VAL* 6.1 0.7 - - - -
165A LYS* 3.2 22.6 - - - +
166A LEU 3.1 25.7 + - - +
167A LEU* 4.2 7.3 - - + +
202A HIS 3.7 0.2 - - - +
203A VAL* 3.2 6.5 - - - +
204A ASP* 2.9 56.3 + - + +
216B LEU* 3.1 41.6 - - + +
217B PRO 3.1 18.5 - - - +
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Residues in contact with ILE 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A GLN* 1.4 74.0 - - - +
110A ARG* 1.3 73.7 + - - +
111A VAL* 5.6 1.1 - - + -
123A VAL* 4.2 30.1 - - + +
124A THR* 4.8 6.7 - - - +
125A VAL* 4.2 14.4 - - + +
149A PRO 5.7 2.7 - - - +
151A LEU* 3.8 31.4 - - + +
165A LYS* 3.4 16.6 - - - -
166A LEU* 3.7 25.2 + - + -
167A LEU 4.9 5.6 - - - +
185A VAL* 5.6 0.9 - - + -
201A LEU* 5.8 2.9 - - + -
202A HIS 3.0 13.5 - - - +
203A VAL* 3.8 18.6 - - + -
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Residues in contact with ARG 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A SER* 4.2 6.7 + - - -
108A GLN* 3.1 27.1 - - + +
109A ILE* 1.3 82.8 - - - +
111A VAL* 1.3 63.6 + - - +
112A ASN* 4.9 9.0 + - - +
164A ASN* 2.9 17.3 - - + +
165A LYS* 4.2 2.7 - - + -
200A VAL 3.8 1.2 - - - +
201A LEU* 3.7 4.0 - - - +
202A HIS* 2.9 61.8 + - + +
204A ASP* 2.8 31.2 + - - -
217B PRO* 3.7 12.6 - - - +
218B VAL* 3.1 46.0 + - - +
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Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ILE* 5.6 0.9 - - + -
110A ARG* 1.3 71.4 - - - +
112A ASN* 1.3 72.4 + - - +
113A PRO* 4.1 3.8 - - - +
123A VAL* 4.4 8.7 - - + -
151A LEU* 3.7 23.6 - - + -
153A TYR* 3.5 49.3 - - + -
164A ASN* 3.3 24.8 + - + +
199A LEU* 3.6 20.4 - - + -
200A VAL 3.8 2.9 - - - -
201A LEU* 3.4 22.7 - - + -
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Residues in contact with ASN 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ARG* 4.9 9.9 + - - +
111A VAL* 1.3 84.1 + - - +
113A PRO* 1.3 70.7 - - + +
114A LEU* 3.5 1.5 + - + +
164A ASN* 5.4 1.4 - - - +
199A LEU* 3.2 4.1 - - - -
200A VAL* 2.8 43.7 + - + +
202A HIS* 3.4 30.1 + - - -
218B VAL* 5.7 4.2 - - - +
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Residues in contact with PRO 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A VAL* 4.1 3.3 - - - +
112A ASN* 1.3 85.9 - - + +
114A LEU* 1.3 63.2 + - - +
115A PRO 4.1 0.3 - - - -
117A PHE* 3.8 18.6 - - + -
153A TYR* 3.2 32.5 - - + +
156A ALA* 3.9 19.5 - - + +
164A ASN* 5.9 0.9 - - - +
198A GLU 3.8 6.3 - - - +
199A LEU* 4.0 4.7 - - + -
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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