Contacts of the strand formed by residues 123 - 129 (chain A) in PDB entry 3FTF
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 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A LEU* 3.4 33.9 - - + +
27A ASN* 4.6 3.1 - - - +
96A LEU 4.5 0.2 + - - -
97A LYS* 3.6 31.3 - - + +
98A VAL 3.2 22.0 + - - +
121A VAL* 3.3 7.0 - - - +
122A PRO* 1.3 94.2 - - + +
124A ALA* 1.3 61.0 + - - +
125A VAL* 5.2 0.7 - - + -
153A TYR* 4.9 0.4 - - - -
178A LYS* 3.9 28.0 - - + +
179A LEU 3.3 12.6 - - - +
180A VAL* 4.5 10.1 - - + -
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Residues in contact with ALA 124 (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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98A VAL* 3.1 20.0 - - + +
114A THR* 5.5 3.4 - - - +
121A VAL* 4.3 6.5 - - + -
123A LEU* 1.3 74.7 - - - +
125A VAL* 1.3 64.4 + - - +
126A PHE* 3.6 31.4 - - + -
153A TYR* 5.2 2.0 - - + -
177A ILE 3.9 0.7 - - - +
178A LYS* 3.5 1.6 - - - +
179A LEU* 2.6 49.3 + - + +
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Residues in contact with VAL 125 (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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22A ILE* 4.1 22.2 - - + +
25A GLU* 4.2 22.9 - - + +
26A LEU* 3.9 23.3 - - + -
98A VAL 3.1 6.5 + - - -
99A VAL* 3.3 9.3 - - + +
100A GLY 3.2 23.4 + - - +
123A LEU* 5.2 1.6 - - + -
124A ALA* 1.3 77.9 - - - +
126A PHE* 1.3 64.8 + - - +
176A VAL* 3.7 26.5 - - + -
177A ILE 3.4 5.4 - - - +
178A LYS* 3.8 21.3 - - + -
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Residues in contact with PHE 126 (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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22A ILE* 6.1 1.8 - - - -
37A VAL* 4.0 15.5 - - + -
98A VAL* 3.8 24.0 - - + -
99A VAL 4.6 0.4 - - - -
100A GLY 3.5 14.1 - - - +
102A LEU* 3.8 17.0 - - + -
110A ILE* 4.4 4.9 - - + -
111A ILE* 4.3 17.0 - - + -
114A THR* 3.9 20.4 - - + -
124A ALA* 3.6 26.5 - - + -
125A VAL* 1.3 80.3 - - - +
127A MET* 1.3 59.3 + - - +
128A VAL* 3.9 17.0 - - + -
175A ALA 3.5 1.0 - - - +
176A VAL* 3.2 7.7 - - - +
177A ILE* 2.8 43.5 + - + +
179A LEU* 3.9 29.2 - - + -
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Residues in contact with MET 127 (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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13A LEU* 3.6 32.1 - - + -
18A VAL* 3.9 1.1 - - + -
22A ILE* 3.8 19.2 - - + +
100A GLY 3.2 8.3 + - - -
101A ASN* 3.3 33.7 - - + +
102A LEU* 3.0 29.5 + - - +
126A PHE* 1.3 70.8 - - - +
128A VAL* 1.3 59.2 - - - +
161A VAL* 3.5 38.4 - - + -
166A PHE* 4.3 5.2 - - + -
174A SER* 3.9 23.6 - - - +
175A ALA 3.4 8.1 - - - +
176A VAL* 3.8 9.6 - - + +
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Residues in contact with VAL 128 (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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102A LEU* 3.6 32.1 - - + -
107A ALA* 4.3 6.3 - - + -
111A ILE* 3.9 17.3 - - + -
126A PHE* 4.2 6.7 - - + -
127A MET* 1.3 77.0 - - - +
129A GLN* 1.3 65.1 + - - +
132A VAL* 4.4 7.2 - - + -
133A ALA* 3.6 28.9 - - + +
174A SER* 3.3 7.8 - - - -
175A ALA 2.8 35.4 + - - +
177A ILE* 3.9 21.1 - - + -
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Residues in contact with GLN 129 (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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102A LEU 5.7 0.8 + - - -
104A TYR* 4.7 22.5 - - + +
107A ALA* 5.5 3.5 - - + +
128A VAL* 1.3 75.1 - - - +
130A LYS* 1.3 78.8 + - - +
131A GLU* 3.2 41.0 + - - +
132A VAL* 2.9 22.2 + - + +
133A ALA 2.8 23.7 + - - -
172A VAL* 3.4 46.8 - - + +
173A GLN 3.7 5.4 + - - +
174A SER* 4.6 2.9 - - - +
1518D A 3.6 13.9 + - - +
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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