Contacts of the strand formed by residues 85 - 97 (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 ASN 85 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ASN* 4.6 2.9 + - - -
79A TRP 3.4 8.1 - - - +
80A LYS* 3.5 28.9 - - + +
84A ARG* 1.3 81.8 - - - +
86A ALA* 1.3 58.6 + - - +
87A HIS* 3.0 42.2 + - + +
88A SER 4.8 0.2 + - - -
61B ASP* 2.9 26.8 + - - +
63B ALA* 3.1 19.2 + - - +
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ASN* 3.4 46.2 + - - +
79A TRP* 2.9 15.6 + - + +
84A ARG 4.3 0.2 - - - -
85A ASN* 1.3 71.6 - - - +
87A HIS* 1.3 73.0 + - - +
88A SER* 3.4 18.7 + - - +
112A SER* 5.3 1.7 + - - -
5100A BTN 3.8 9.5 + - - +
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Residues in contact with HIS 87 (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 4.4 0.2 + - - -
85A ASN* 3.0 32.8 + - + +
86A ALA* 1.3 82.0 - - - +
88A SER* 1.3 58.6 + - - +
112A SER* 3.6 2.4 - - - -
113A GLY* 2.9 31.8 + - - +
61B ASP* 2.7 29.8 + - - +
63B ALA 3.1 22.6 + - - -
64B PRO 3.7 0.7 - - - -
65B ALA* 3.4 35.8 + - + +
72B ALA* 4.1 5.4 - - - -
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Residues in contact with SER 88 (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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78A ALA* 3.6 3.5 - - - +
79A TRP* 2.9 40.3 + - - +
85A ASN* 4.8 0.4 + - - -
86A ALA* 3.5 6.2 - - - +
87A HIS* 1.3 79.0 - - - +
89A ALA* 1.3 63.5 + - - +
110A LEU* 3.9 4.9 - - - -
111A THR 3.2 14.1 - - - -
112A SER* 3.8 12.8 - - - -
5100A BTN 2.8 27.5 + - - -
61B ASP* 4.6 3.3 + - - +
72B ALA* 3.5 8.4 - - - +
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Residues in contact with ALA 89 (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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76A THR* 4.6 2.7 - - + -
77A VAL 3.2 13.9 - - - +
78A ALA* 4.0 8.5 - - + -
79A TRP* 3.7 2.0 - - - -
88A SER* 1.3 77.6 - - - +
90A THR* 1.3 63.6 + - - +
109A LEU 3.7 1.2 - - - +
110A LEU* 3.4 1.5 - - - -
111A THR* 2.9 32.0 + - - +
72B ALA* 3.8 1.5 - - + +
73B LEU* 3.9 38.4 - - - +
74B GLY* 4.3 2.2 - - - +
93B SER* 3.7 4.0 + - - +
94B GLY 5.5 0.2 - - - +
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Residues in contact with THR 90 (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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76A THR* 3.3 4.6 - - - +
77A VAL 2.8 32.5 + - - +
79A TRP* 2.9 21.8 + - - +
89A ALA* 1.3 72.9 - - - +
91A THR* 1.3 70.4 + - - +
92A TRP* 3.6 34.4 - - + -
108A TRP* 3.9 12.6 - - + -
109A LEU 3.2 12.1 - - - +
110A LEU* 3.3 15.4 - - - +
5100A BTN 3.4 18.3 - - + -
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Residues in contact with THR 91 (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 3.2 5.2 - - - -
76A THR* 3.3 22.4 - - - +
89A ALA 5.7 0.2 - - - -
90A THR* 1.3 77.6 - - - +
92A TRP* 1.3 60.3 + - - +
107A GLN 4.0 0.2 - - - +
108A TRP* 3.0 5.7 - - - +
109A LEU* 3.0 34.1 + - - +
74B GLY* 3.7 9.2 - - - -
75B TRP 4.1 1.3 - - - +
91B THR* 3.1 28.2 + - - -
92B TRP 3.3 25.6 - - - +
93B SER* 3.6 18.0 + - - -
109B LEU* 4.8 0.7 - - - +
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Residues in contact with TRP 92 (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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43A TYR* 3.4 33.9 - + - -
74A GLY* 3.0 25.5 - - - -
75A TRP* 2.9 61.0 + + + -
77A VAL* 3.7 15.0 - - + -
79A TRP* 3.8 19.5 - + - -
90A THR* 3.6 34.1 - - + -
91A THR* 1.3 72.8 - - - +
93A SER* 1.3 59.8 + - - +
106A THR* 3.4 26.0 - - + -
107A GLN 3.5 4.9 - - - +
108A TRP* 3.7 12.8 - - + -
128A ASP* 2.9 21.2 + - - -
130A PHE* 3.8 12.1 - + - -
5100A BTN 3.8 18.4 - - + -
91B THR* 3.3 3.6 - - - +
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Residues in contact with SER 93 (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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73A LEU 3.7 5.3 + - - -
92A TRP* 1.3 74.5 - - - +
94A GLY* 1.3 59.6 + - - +
106A THR* 3.4 2.9 - - - -
107A GLN* 2.9 32.0 + - - +
89B ALA 3.7 5.0 + - - -
91B THR* 3.5 22.0 + - - +
109B LEU* 3.1 32.8 + - - -
111B THR* 2.8 27.6 + - - -
123B THR* 5.4 0.4 + - - -
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Residues in contact with GLY 94 (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 ALA* 3.5 3.8 - - - -
73A LEU* 3.0 37.7 + - - +
74A GLY* 4.9 0.2 - - - -
93A SER* 1.3 77.9 + - - +
95A GLN* 1.3 63.9 + - - +
105A ASN 3.1 13.0 - - - -
106A THR* 4.1 3.7 - - - +
111B THR* 3.5 19.5 + - - +
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Residues in contact with GLN 95 (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 GLY* 3.2 11.1 - - - -
71A THR 3.1 16.8 - - - +
72A ALA* 4.4 2.2 - - - -
73A LEU* 3.5 6.4 - - - +
94A GLY* 1.3 77.4 - - - +
96A TYR* 1.3 61.3 + - - +
97A VAL* 3.9 12.7 + - + +
103A ARG 3.9 0.2 - - - +
104A ILE* 3.4 1.9 - - - -
105A ASN* 3.0 41.8 + - + +
111B THR* 4.6 3.7 - - + +
112B SER 3.8 4.2 + - - -
113B GLY* 3.3 2.2 - - - -
114B THR* 2.8 52.4 + - - +
119B ALA* 4.3 9.7 - - - +
122B SER* 3.7 21.4 + - - -
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Residues in contact with TYR 96 (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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14A GLU 5.9 1.3 - - - -
16A GLY* 3.2 42.4 + - - -
17A ILE* 3.7 26.5 - - + -
21A TRP* 3.8 25.4 - + - -
70A GLY* 3.3 4.9 - - - -
71A THR* 2.8 49.8 + - - +
73A LEU* 3.7 9.7 - - + +
95A GLN* 1.3 71.5 - - - +
97A VAL* 1.3 61.5 + - - +
98A GLY* 3.3 28.8 + - - -
99A GLY 4.3 2.6 + - - -
102A ALA* 4.0 12.1 - - + +
103A ARG 3.5 5.2 - - - -
104A ILE* 4.0 5.6 - - + -
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Residues in contact with VAL 97 (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 GLY* 4.7 8.7 - - - +
95A GLN* 4.3 15.3 - - + +
96A TYR* 1.3 77.6 - - - +
98A GLY* 1.3 68.1 + - - +
101A GLU 4.4 1.6 - - - +
102A ALA* 3.3 4.2 - - - +
103A ARG* 2.8 42.6 + - + +
105A ASN* 3.9 22.4 - - - +
114B THR 5.9 1.1 - - - +
116B GLU* 6.1 8.1 - - + -
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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