Contacts of the strand formed by residues 82 - 91 (chain A) in PDB entry 2F24
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 HIS 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49A ALA* 4.2 13.8 - - - +
50A GLU 4.6 0.9 - - - +
51A LEU* 5.6 1.7 - - - +
78A ARG* 5.1 4.0 - - - +
79A LEU* 2.9 37.8 + - + +
80A ASP 2.9 24.3 + - - -
81A GLY* 1.3 83.5 - - - +
83A ARG* 1.3 60.6 + - - +
84A SER* 4.1 2.9 + - - -
104A ALA* 3.8 15.9 - - + -
105A ILE* 3.2 16.6 - - - +
106A PRO* 3.4 37.6 - - + +
107A GLY* 4.6 2.0 - - - -
121A VAL 4.7 0.8 + - - -
123A ARG* 4.3 14.0 - - + +
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Residues in contact with ARG 83 (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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49A ALA* 4.7 3.1 - - + -
50A GLU* 3.6 44.8 + - + +
82A HIS* 1.3 73.8 - - - +
84A SER* 1.3 61.6 + - - +
85A MET* 3.4 26.5 - - + +
103A ILE 3.5 0.9 - - - +
104A ALA* 3.3 5.9 - - - -
105A ILE* 2.7 46.8 + - - +
106A PRO 3.9 12.3 + - - -
107A GLY* 4.3 16.3 + - - +
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Residues in contact with SER 84 (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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39A GLU* 4.2 3.5 - - - +
50A GLU* 2.9 38.3 + - - +
51A LEU* 4.2 6.6 + - - +
52A ILE* 4.1 13.7 - - - -
77A ALA 2.7 28.4 + - - -
78A ARG* 3.3 18.5 - - - +
79A LEU 4.6 0.7 + - - -
82A HIS 4.1 0.8 + - - -
83A ARG* 1.3 72.3 - - - +
85A MET* 1.3 61.8 + - - +
102A PHE* 3.7 12.6 - - - -
103A ILE 3.4 4.9 - - - -
104A ALA* 5.1 1.0 - - - +
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Residues in contact with MET 85 (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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39A GLU* 3.2 19.1 - - - +
50A GLU* 3.2 16.2 - - - +
52A ILE* 4.6 2.6 - - - +
83A ARG* 3.4 49.8 - - + +
84A SER* 1.3 74.0 - - - +
86A ASN* 1.3 76.9 + - - +
87A PRO* 3.6 2.2 - - - -
102A PHE* 3.5 3.6 - - - +
103A ILE* 2.9 50.3 + - + +
105A ILE* 3.8 28.9 - - + -
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Residues in contact with ASN 86 (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* 4.2 8.6 - - - +
39A GLU* 2.7 25.3 + - - -
85A MET* 1.3 88.0 - - - +
87A PRO* 1.3 73.2 - - - +
88A CYS* 3.2 12.1 + - - -
101A PHE 3.5 5.4 - - - +
102A PHE* 3.7 3.1 - - - -
103A ILE* 4.2 10.5 - - + +
158A ALA* 3.6 20.1 - - - +
159A VAL* 3.0 24.1 - - - +
160A GLY 4.0 0.5 - - - +
161A PRO* 3.7 20.7 - - + +
179A TYR* 4.8 3.9 + - - -
218A GLU* 5.3 0.9 - - - +
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Residues in contact with PRO 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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22A ILE* 3.6 26.9 - - + +
24A ALA* 3.4 12.5 - - + +
37A PHE* 3.8 24.9 - - + -
38A ALA* 4.3 6.7 - - - +
39A GLU* 4.1 12.6 - - + -
52A ILE* 3.9 23.3 - - + -
85A MET 3.6 2.4 - - - -
86A ASN* 1.3 88.9 - - - +
88A CYS* 1.3 57.4 + - - +
89A PRO* 3.8 2.5 - - - -
100A LEU* 4.0 8.1 - - + -
101A PHE 3.7 4.7 - - - +
161A PRO* 4.0 0.3 - - - +
162A GLY 3.1 22.0 + - - -
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Residues in contact with CYS 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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86A ASN 3.2 15.3 - - - -
87A PRO* 1.3 74.3 - - - +
89A PRO* 1.3 63.3 - - - +
100A LEU* 3.7 2.1 - - - +
101A PHE* 2.8 53.4 + - + +
159A VAL* 3.1 44.0 - - + -
160A GLY* 3.3 13.5 - - - -
161A PRO* 3.8 1.1 - - - -
162A GLY 3.2 11.0 - - - +
164A CYS* 3.7 11.4 - - - -
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Residues in contact with PRO 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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24A ALA* 3.5 23.1 - - + -
25A LEU 4.1 9.2 - - - +
26A LEU* 3.9 28.2 - - + +
37A PHE* 3.7 30.1 - - + -
87A PRO 3.8 0.2 - - - -
88A CYS* 1.3 87.8 - - - +
90A LEU* 1.3 61.6 + - - +
99A PHE 3.2 9.2 - - - +
100A LEU* 4.1 6.3 - - + -
136A TRP* 6.3 0.2 - - + -
162A GLY 3.6 7.4 - - - +
163A HIS* 3.3 4.8 - - - +
164A CYS 2.8 27.5 + - - -
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Residues in contact with LEU 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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26A LEU* 3.9 11.1 - - + +
89A PRO* 1.3 76.9 - - - +
91A TYR* 1.3 79.7 + - - +
92A ASP 4.1 1.1 + - - +
97A THR 4.1 0.2 - - - +
98A LEU* 3.4 4.0 - - - -
99A PHE* 2.8 47.9 + - + +
101A PHE* 4.5 9.9 - - + -
164A CYS* 3.8 35.4 - - + +
165A LEU 3.8 21.8 - - - +
166A GLN* 4.1 5.2 - - + +
174A LEU* 3.7 39.3 - - + -
175A VAL 4.9 0.7 - - - +
176A VAL* 5.3 0.7 - - + -
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Residues in contact with TYR 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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26A LEU* 3.8 16.0 - - + +
27A TYR 4.2 6.7 - - - +
28A LEU* 4.3 5.8 - - + -
29A PRO* 3.5 35.7 - - + +
30A GLY* 5.1 2.1 + - - -
90A LEU* 1.3 88.4 - - - +
92A ASP* 1.3 67.0 + - - +
93A ALA* 3.5 36.9 + - + +
96A GLY* 3.9 17.8 - - - -
97A THR 3.9 1.6 - - - -
98A LEU* 3.5 24.7 - - + -
166A GLN* 3.4 10.7 - - - +
1001A CL 3.9 15.9 - - + -
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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