Contacts of the strand formed by residues 113 - 122 (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 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A VAL* 4.5 3.8 - - + -
108A LYS* 5.2 0.2 + - - -
109A GLN* 3.5 1.6 - - - +
110A GLY* 2.8 30.1 + - - +
111A LYS 3.8 0.2 - - - -
112A THR* 1.3 91.0 - - - +
114A ALA* 1.3 59.5 + - - +
115A PHE* 4.0 19.5 - - + -
135A THR* 4.2 12.8 - - + -
136A LYS 3.4 13.9 - - - +
137A HIS* 4.1 13.0 - - + +
138A LEU* 4.3 2.9 - - - -
84C VAL* 3.9 22.7 - - + -
113C LEU* 4.2 18.2 - - + -
137C HIS* 4.1 11.4 - - + +
150C COA 3.0 41.8 + - + +
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Residues in contact with ALA 114 (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 LEU* 3.6 33.9 - - + -
108A LYS 3.5 4.3 - - - -
109A GLN* 3.8 11.7 - - + -
113A LEU* 1.3 75.0 - - - +
115A PHE* 1.3 63.9 + - - +
116A THR* 5.0 1.6 - - - -
134A HIS 3.9 0.6 - - - +
135A THR* 3.3 6.2 - - - +
136A LYS* 2.9 32.5 + - - +
138A LEU* 4.0 18.8 - - + -
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Residues in contact with PHE 115 (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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106A VAL* 3.7 1.7 - - - +
107A LEU* 2.7 31.7 + - + -
108A LYS* 2.9 35.2 + - + +
113A LEU* 4.0 24.0 - - + -
114A ALA* 1.3 73.4 - - - +
116A THR* 1.3 61.1 + - - +
133A ARG* 5.9 0.9 - - + -
134A HIS 3.7 2.5 - - - -
135A THR* 3.4 26.9 - - + -
84C VAL* 3.7 17.9 - - + -
150C COA 3.5 28.3 - - - -
89D THR* 3.3 31.6 - - + -
90D TYR 3.8 11.0 - - - -
91D MET* 3.7 32.5 - - + -
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Residues in contact with THR 116 (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 SER* 3.2 33.7 - - - +
71A ALA* 5.4 0.2 - - + -
72A LEU* 3.8 38.8 - - + -
105A HIS 3.3 13.5 - - - +
106A VAL* 4.2 6.1 - - + -
107A LEU* 4.0 4.5 - - - +
114A ALA 5.0 0.2 - - - -
115A PHE* 1.3 81.8 - - - +
117A SER* 1.3 60.4 + - - +
133A ARG* 3.1 9.2 - - - +
134A HIS* 2.9 46.9 + - - +
136A LYS* 5.5 0.2 - - - +
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Residues in contact with SER 117 (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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104A ALA* 3.4 2.4 - - - -
105A HIS* 2.9 53.8 + - - -
107A LEU* 3.9 18.8 - - - +
116A THR* 1.3 74.9 - - - +
118A VAL* 1.3 66.9 + - - +
119A ASP* 4.6 1.9 + - - -
131A GLN* 4.4 14.0 + - - +
132A GLY 3.4 11.1 + - - -
133A ARG* 4.4 0.7 - - - +
131D GLN* 3.9 15.7 + - - -
133D ARG* 5.4 0.2 + - - -
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Residues in contact with VAL 118 (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* 3.7 31.6 - - + +
68A SER* 3.7 28.0 - - - +
102A ILE* 3.5 32.8 - - + -
103A THR 3.2 9.9 - - - +
104A ALA* 3.8 9.9 - - + -
116A THR* 5.1 0.4 - - - +
117A SER* 1.3 82.1 + - - +
119A ASP* 1.3 68.2 + - - +
120A LEU* 4.1 11.9 - - + +
130A ALA 4.1 0.2 - - - +
131A GLN* 3.3 4.3 - - - +
132A GLY 2.9 32.8 + - - +
134A HIS* 5.8 0.2 - - + -
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Residues in contact with ASP 119 (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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101A VAL 3.6 1.6 - - - +
102A ILE* 3.6 2.1 - - - -
103A THR* 2.9 40.6 + - + +
117A SER* 4.6 2.6 + - - -
118A VAL* 1.3 73.0 - - - +
120A LEU* 1.3 62.4 + - - +
121A THR* 4.5 9.1 - - + +
128A LEU* 3.8 21.7 - - + +
130A ALA 3.6 3.8 - - - -
131A GLN* 2.9 35.3 - - - +
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Residues in contact with LEU 120 (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* 4.3 8.1 - - + -
60A THR* 3.8 26.2 - - + +
63A LEU* 4.1 24.7 - - + -
64A VAL* 4.0 27.6 - - + +
100A ILE* 4.1 15.3 - - + -
101A VAL 3.3 4.3 - - - +
102A ILE* 4.0 13.5 - - + -
118A VAL* 4.1 9.2 - - + +
119A ASP* 1.3 77.0 - - - +
121A THR* 1.3 59.2 + - - +
128A LEU* 3.7 1.4 - - - +
129A ILE* 2.7 45.2 + - + -
130A ALA* 2.9 21.7 + - + +
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Residues in contact with THR 121 (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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100A ILE* 3.3 5.5 - - - -
101A VAL* 2.8 51.3 + - - +
103A THR* 5.2 1.9 + - - -
119A ASP* 4.5 9.8 + - + +
120A LEU* 1.3 80.1 - - - +
122A ASN* 1.3 64.5 + - - +
126A GLY* 3.7 21.7 - - - +
127A LYS 3.4 7.4 - - - +
128A LEU* 4.0 18.8 - - + -
129A ILE* 3.4 7.1 - - - +
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Residues in contact with ASN 122 (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 GLU* 2.8 35.3 + - - +
99A ASP 3.8 6.5 + - - +
121A THR* 1.3 72.7 + - - +
123A LYS* 1.3 58.6 + - - +
124A ALA* 2.9 17.9 + - - +
125A THR* 2.8 48.8 + - - +
126A GLY* 2.7 30.5 + - - -
127A LYS* 2.9 20.9 + - + +
129A ILE* 3.5 10.8 - - + +
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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