Contacts of the strand formed by residues 103 - 112 (chain A) in PDB entry 2F01
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 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A TRP* 3.7 2.2 - - - -
95A GLN 3.9 0.6 - - - +
96A TYR* 3.5 3.3 - - - -
97A VAL* 2.8 39.3 + - + +
101A GLU* 3.4 35.0 + - - +
102A ALA* 1.3 89.6 + - - +
104A ILE* 1.3 64.3 + - - +
105A ASN* 4.0 21.3 - - - +
129A THR* 4.2 13.7 - - - +
130A PHE 3.2 13.9 - - - +
131A THR* 3.5 32.5 + - - +
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Residues in contact with ILE 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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17A ILE* 4.7 6.7 - - + -
21A TRP* 3.6 39.0 - - + +
29A PHE* 3.9 18.8 - - + -
73A LEU* 4.1 27.6 - - + -
75A TRP* 4.2 9.2 - - + -
95A GLN 3.4 8.7 - - - +
96A TYR* 4.0 14.4 - - + -
103A ARG* 1.3 76.5 - - - +
105A ASN* 1.3 63.2 + - - +
106A THR* 3.7 20.6 - - + -
129A THR* 3.6 1.7 - - - -
130A PHE* 2.8 47.5 + - + -
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Residues in contact with ASN 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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94A GLY* 3.1 3.5 - - - -
95A GLN* 3.0 38.1 + - + +
97A VAL* 3.9 23.8 - - - +
103A ARG* 4.0 11.6 - - - +
104A ILE* 1.3 73.7 - - - +
106A THR* 1.3 58.3 + - - +
128A ASP 4.0 2.5 - - - -
129A THR* 3.2 30.5 + - - +
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Residues in contact with THR 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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75A TRP* 3.8 21.3 - - + -
92A TRP* 3.4 24.4 - - + -
93A SER 3.4 11.0 - - - +
94A GLY* 4.4 3.6 - - - -
104A ILE* 3.7 22.4 - - + -
105A ASN* 1.3 79.3 - - - +
107A GLN* 1.3 68.4 + - - +
127A HIS* 3.3 10.6 - - - +
128A ASP* 2.8 41.9 + - - +
130A PHE* 4.1 5.6 - - + -
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Residues in contact with GLN 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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92A TRP* 3.5 2.4 - - - -
93A SER 2.9 32.9 + - - +
106A THR* 1.3 77.8 - - - +
108A TRP* 1.3 61.1 + - - +
125A VAL* 4.5 11.3 - - - +
126A GLY 3.3 24.0 + - - -
127A HIS* 4.1 15.3 - - - +
109B LEU* 3.5 23.5 - - + +
123B THR* 4.5 24.1 + - + +
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Residues in contact with TRP 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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25A LEU* 6.0 1.3 - - + -
90A THR* 3.9 4.9 - - + -
91A THR 3.0 14.6 - - - +
92A TRP* 3.7 16.8 - + + -
107A GLN* 1.3 75.7 - - - +
109A LEU* 1.3 67.5 + - - +
110A LEU* 3.8 24.9 - - + -
124A LEU* 3.7 26.0 - - + -
125A VAL* 3.3 17.0 - - - +
126A GLY* 2.9 54.6 + - - -
127A HIS 3.3 8.9 + - - +
128A ASP* 3.0 44.7 + - - -
5100A BTN 3.4 29.2 - + + -
109B LEU* 4.0 1.6 - - - -
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Residues in contact with LEU 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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90A THR* 3.2 1.2 - - - -
91A THR* 3.0 34.4 + - - +
108A TRP* 1.3 83.8 - - - +
110A LEU* 1.3 60.1 + - - +
123A THR* 4.1 13.7 - - + -
124A LEU 3.3 4.3 - - - +
125A VAL* 4.0 21.8 - - + -
91B THR 4.9 0.2 - - - +
93B SER* 3.1 22.6 + - - +
107B GLN* 3.5 43.7 - - + +
108B TRP* 3.9 4.7 - - - +
109B LEU* 3.8 29.2 - - + +
125B VAL* 5.6 4.5 - - + -
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Residues in contact with LEU 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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79A TRP* 4.0 5.2 - - - +
88A SER* 3.9 23.8 - - - -
89A ALA 3.4 9.4 - - - +
90A THR* 3.3 21.3 - - - +
108A TRP* 3.8 18.8 - - + -
109A LEU* 1.3 70.4 - - - +
111A THR* 1.3 61.7 + - - +
112A SER* 4.0 5.5 + - - +
122A SER 3.5 2.3 - - - +
123A THR* 3.2 3.1 - - - -
124A LEU* 2.9 60.4 + - + +
5100A BTN 3.9 38.1 - - + +
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Residues in contact with THR 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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88A SER* 3.2 3.5 - - - -
89A ALA 2.9 33.0 + - - -
110A LEU* 1.3 71.9 - - - +
112A SER* 1.3 73.9 + - - +
122A SER* 3.3 10.5 - - - +
123A THR* 3.3 25.2 + - - +
72B ALA* 3.6 4.2 - - - +
73B LEU 5.1 0.4 - - - -
93B SER* 2.8 27.2 + - - -
94B GLY* 3.4 37.6 + - - +
95B GLN* 4.3 5.6 - - + +
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Residues in contact with SER 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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86A ALA 5.3 1.4 + - - -
87A HIS 3.6 8.3 - - - -
88A SER* 3.8 10.9 - - - -
110A LEU* 4.0 6.1 + - - +
111A THR* 1.3 80.8 - - - +
113A GLY* 1.3 69.2 + - - +
114A THR* 3.4 16.6 + - - +
122A SER* 2.9 23.3 + - - -
5100A BTN 4.8 3.3 + - - -
72B ALA* 4.5 0.4 - - - -
95B GLN* 3.8 1.7 - - - +
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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