Contacts of the strand formed by residues 128 - 137 (chain A) in PDB entry 3F5O
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 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A MET* 3.8 29.8 - - + +
92A SER* 2.8 24.6 + - - -
119A ASP* 3.8 28.9 - - + +
120A LEU 3.7 14.8 - - - +
121A THR* 4.0 8.3 - - + -
126A GLY 3.7 1.4 + - - -
127A LYS* 1.3 74.8 - - - +
129A ILE* 1.3 55.3 + - - +
130A ALA 3.7 17.3 - - - +
131A GLN* 4.8 4.3 - - + +
107D LEU* 3.9 47.1 - - + +
108D LYS* 5.7 2.3 - - + +
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Residues in contact with ILE 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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55A LEU* 4.8 10.1 - - + -
60A THR* 5.3 2.0 - - - +
90A TYR* 3.7 3.3 - - + +
91A MET* 2.8 25.7 + - - -
92A SER* 3.2 29.4 + - - +
93A PRO 4.9 1.1 - - - +
94A ALA* 3.9 22.4 - - + +
98A GLU* 4.7 1.8 - - - +
100A ILE* 3.4 35.9 - - + -
120A LEU* 2.7 21.7 + - + +
121A THR* 3.4 23.3 - - - +
122A ASN* 3.5 12.6 - - + +
127A LYS* 3.4 1.7 + - + +
128A LEU* 1.3 73.5 - - - +
130A ALA* 1.3 66.4 + - + +
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Residues in contact with ALA 130 (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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60A THR* 3.8 28.7 - - + -
88A ILE* 4.2 6.7 - - + -
89A THR 3.1 16.4 - - - +
90A TYR* 4.4 5.4 - - + -
91A MET* 3.9 4.9 - - - -
119A ASP* 3.6 1.7 - - - -
120A LEU* 2.9 33.0 + - + +
128A LEU* 3.7 5.5 - - - +
129A ILE* 1.3 86.3 - - + +
131A GLN* 1.3 62.0 + - - +
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Residues in contact with GLN 131 (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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64A VAL* 5.4 0.4 - - - -
88A ILE* 3.4 4.1 - - - -
89A THR* 2.8 30.9 + - - -
91A MET* 4.0 12.5 - - + -
117A SER* 4.4 9.1 + - - +
118A VAL 3.3 5.8 - - - +
119A ASP* 2.9 28.7 - - - +
128A LEU* 4.8 4.6 - - + +
130A ALA* 1.3 75.6 - - - +
132A GLY* 1.3 64.5 + - - +
133A ARG* 5.5 0.6 - - - +
107D LEU* 3.7 22.1 - - - +
117D SER* 4.1 10.1 + - - -
131D GLN* 5.3 7.0 - - - +
132D GLY 5.7 0.2 + - - -
133D ARG* 2.8 45.3 - - - +
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Residues in contact with GLY 132 (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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64A VAL* 4.4 20.7 - - - +
87A ASN 3.0 13.7 - - - -
88A ILE* 4.1 2.0 - - - -
117A SER* 3.4 8.5 + - - -
118A VAL 2.9 34.5 + - - -
131A GLN* 1.3 74.6 - - - +
133A ARG* 1.3 60.0 + - - -
133D ARG* 3.4 7.7 + - - -
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Residues in contact with ARG 133 (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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85A ASP 4.6 0.6 - - - -
86A MET* 3.3 7.6 - - - +
87A ASN* 3.0 45.7 + - - +
107A LEU* 4.1 3.1 - - + -
115A PHE* 5.9 0.7 - - + -
116A THR 3.1 20.4 - - - +
117A SER* 4.5 0.2 - - - -
131A GLN* 5.5 0.8 - - - +
132A GLY* 1.3 74.9 - - - +
134A HIS* 1.3 63.2 + - - +
135A THR* 5.8 0.9 - - - +
87D ASN* 2.9 30.8 + - - -
88D ILE 4.2 0.8 - - - -
89D THR* 2.8 48.6 + - + +
91D MET* 3.9 10.3 - - - -
131D GLN* 2.8 43.7 + - - +
132D GLY* 3.4 25.3 + - - +
133D ARG* 3.3 19.4 - - - +
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Residues in contact with HIS 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A VAL* 4.4 7.2 - - + -
65A ASP* 3.8 27.8 + - + -
68A SER* 2.8 24.9 + - - +
69A THR* 4.0 0.2 - - - -
83A SER* 2.7 32.1 + - - -
85A ASP 3.5 10.1 - - - -
86A MET* 3.9 15.0 - - + -
114A ALA 3.9 0.9 - - - +
115A PHE* 3.7 1.2 - - - -
116A THR* 2.9 48.7 + - - +
118A VAL* 5.8 0.2 - - + -
133A ARG* 1.3 77.9 - - - +
135A THR* 1.3 70.9 + - - +
136A LYS* 3.5 28.9 + - + +
149A UOC 5.6 0.2 - - + -
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Residues in contact with THR 135 (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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83A SER 3.8 0.2 - - - -
84A VAL* 2.8 29.9 + - + -
85A ASP 2.8 19.0 + - - +
113A LEU* 4.2 16.4 - - + -
114A ALA 3.3 10.1 - - - +
115A PHE* 3.4 31.3 - - + -
133A ARG* 5.8 0.5 - - - +
134A HIS* 1.3 75.4 - - - +
136A LYS* 1.3 64.8 + - - +
84C VAL* 4.1 9.0 - - + -
85C ASP* 2.8 31.7 + - - +
89D THR* 3.9 2.6 + - - +
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Residues in contact with LYS 136 (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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69A THR* 2.8 29.6 + - - +
72A LEU* 3.7 23.8 - - + -
80A PRO 2.7 28.7 + - - +
81A GLY* 3.1 16.5 + - - -
82A VAL 3.1 14.4 - - - +
84A VAL* 4.0 4.7 - - - +
113A LEU* 3.4 6.7 - - - +
114A ALA* 2.9 34.6 + - + +
116A THR* 5.5 0.4 - - - +
134A HIS* 3.5 36.1 - - + +
135A THR* 1.3 76.9 - - - +
137A HIS* 1.3 59.5 + - - +
138A LEU* 3.9 2.8 + - + +
149A UOC 3.1 27.4 - - - +
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Residues in contact with HIS 137 (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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81A GLY* 3.1 2.3 - - - -
82A VAL* 2.8 45.2 + - + +
84A VAL* 3.5 19.3 - - + +
112A THR* 3.3 28.8 + - + -
113A LEU* 4.1 4.9 - - + +
136A LYS* 1.3 73.0 - - - +
138A LEU* 1.3 60.5 + - - +
139A GLY* 3.3 23.7 + - - -
150A COA 3.7 42.2 + - + +
112C THR* 3.2 29.6 + - + -
113C LEU* 4.1 12.4 - - + +
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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