Contacts of the strand formed by residues 69 - 82 (chain A) in PDB entry 2DT4
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 SER 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A THR* 4.1 14.4 - - - +
46A LEU 3.4 5.4 - - - -
47A LYS* 3.4 29.3 - - - +
67A LYS 5.1 0.2 - - - +
68A GLY* 1.3 71.2 - - - -
70A TYR* 1.3 67.4 + - - +
95A GLY 4.5 2.1 - - - +
96A ASN* 5.1 3.8 - - - -
97A GLU* 5.4 2.1 + - - +
112A PHE* 5.7 0.3 - - - -
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Residues in contact with TYR 70 (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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45A THR* 3.3 5.6 - - - -
46A LEU* 2.9 35.1 + - - +
49A PRO* 4.1 13.0 - - + -
66A LEU* 3.7 34.4 - - + +
67A LYS 3.3 24.4 + - - -
68A GLY 3.7 8.7 - - - -
69A SER* 1.3 80.5 - - - +
71A GLU* 1.3 62.3 + - - +
72A LEU* 3.3 0.3 + - - -
94A LEU* 3.9 32.0 - - + +
95A GLY 3.3 20.2 - - - +
96A ASN* 3.6 23.4 + - + +
102A PHE* 3.8 24.6 - + - -
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Residues in contact with GLU 71 (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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44A GLY 3.5 7.9 - - - +
45A THR* 3.4 19.1 + - - +
70A TYR* 1.3 70.7 - - - +
72A LEU* 1.3 58.1 + - - +
73A ILE* 3.2 12.2 + - + -
94A LEU* 3.1 8.7 - - - -
95A GLY* 2.8 47.4 + - - +
96A ASN 5.7 2.5 - - - +
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Residues in contact with LEU 72 (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 LEU* 4.3 19.1 - - + -
42A GLY 4.6 0.2 - - - -
43A ILE* 3.4 32.9 - - - +
44A GLY* 2.8 39.0 + - - +
45A THR* 3.8 4.9 - - - +
46A LEU* 4.0 18.6 - - + -
70A TYR 3.3 2.2 + - - -
71A GLU* 1.3 68.5 - - - +
73A ILE* 1.3 63.3 + - - +
74A SER 3.4 29.2 - - - +
75A LEU* 4.2 13.0 - - + -
92A VAL* 3.5 26.2 - - + -
93A SER 3.8 3.6 - - - +
94A LEU* 4.0 7.4 - - + -
114A ALA* 4.8 4.9 - - + -
116A ILE* 5.1 1.6 - - + -
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Residues in contact with ILE 73 (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 ILE* 3.5 17.8 - - - +
71A GLU* 3.8 15.5 - - + +
72A LEU* 1.3 73.2 - - - +
74A SER* 1.3 61.8 + - - +
93A SER* 2.9 20.6 + - - +
94A LEU 4.0 1.8 - - - -
95A GLY* 3.5 25.6 - - - +
101A VAL* 3.6 30.3 - - + -
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Residues in contact with SER 74 (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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42A GLY 3.7 5.4 - - - -
72A LEU* 3.5 7.8 - - - +
73A ILE* 1.3 83.0 - - - +
75A LEU* 1.4 63.5 - - - +
76A ILE* 4.2 13.8 - - - +
91A HIS 5.1 0.9 + - - -
92A VAL* 3.2 7.2 - - - -
93A SER* 2.7 42.9 + - - -
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Residues in contact with LEU 75 (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 LEU* 3.5 33.0 - - + -
23A LEU* 5.6 0.4 - - + -
26A ILE* 5.2 4.7 - - + -
40A ILE* 3.9 35.4 - - + -
41A ASN* 3.1 6.9 - - - +
42A GLY* 2.9 46.6 + - - +
72A LEU* 4.2 9.9 - - + -
74A SER* 1.4 59.4 - - - +
76A ILE* 1.3 72.0 + - - +
90A ALA* 4.1 15.3 - - + -
91A HIS 3.5 4.9 - - - +
92A VAL* 3.9 15.5 - - + -
106A LEU* 4.2 3.8 - - + -
116A ILE* 5.0 7.4 - - + -
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Residues in contact with ILE 76 (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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40A ILE 3.5 7.4 - - - +
41A ASN* 4.8 7.2 - - + -
74A SER* 4.8 13.0 - - - +
75A LEU* 1.3 86.3 - - - +
77A GLY* 1.3 64.1 + - - +
90A ALA* 3.4 0.7 - - - -
91A HIS* 3.0 34.0 + - + +
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Residues in contact with GLY 77 (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 ILE* 3.6 6.4 - - - +
40A ILE* 3.0 37.6 + - - +
76A ILE* 1.3 82.2 - - - +
78A ASN* 1.3 69.9 + - - +
89A HIS 3.2 12.8 - - - -
90A ALA* 4.0 1.3 - - - -
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Residues in contact with ASN 78 (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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38A ALA 3.3 13.2 - - - +
39A ILE* 4.2 9.4 - - + +
40A ILE* 3.7 3.8 - - - +
77A GLY* 1.3 79.5 - - - +
79A VAL* 1.3 65.8 + - - +
80A SER* 4.3 2.8 + - - -
87A PHE 3.7 0.2 - - - +
88A VAL* 3.6 4.2 - - - +
89A HIS* 2.9 42.9 + - - +
128A ARG* 2.8 29.1 + - - +
138A TRP* 3.6 34.3 - - + -
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Residues in contact with VAL 79 (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 ILE* 4.2 17.7 - - + -
30A CYS* 3.9 27.4 - - + -
35A ILE* 5.0 0.2 - - + -
36A GLU 3.7 9.6 - - - +
37A THR* 3.2 6.9 - - - +
38A ALA* 2.8 45.1 + - + +
40A ILE* 4.5 9.0 - - + -
78A ASN* 1.3 79.3 - - - +
80A SER* 1.3 67.3 + - - +
86A PRO* 3.8 26.9 - - + -
87A PHE 3.3 11.4 - - - +
88A VAL* 4.3 8.3 - - + -
118A LEU* 4.7 0.2 - - + -
138A TRP* 5.5 0.3 - - - -
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Residues in contact with SER 80 (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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36A GLU 3.1 10.5 - - - -
37A THR* 4.5 1.1 - - - +
78A ASN* 4.3 0.5 + - - -
79A VAL* 1.3 78.6 - - - +
81A LEU* 1.3 63.2 + - - +
86A PRO* 4.5 0.4 - - - -
87A PHE* 2.9 31.8 + - - +
126A ILE* 3.6 17.7 - - - -
128A ARG* 3.5 19.9 + - - +
138A TRP* 2.9 37.6 + - - -
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Residues in contact with LEU 81 (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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36A GLU* 3.5 34.8 + - + +
37A THR* 5.1 0.8 + - - +
80A SER* 1.3 75.7 - - - +
82A LYS* 1.3 59.6 + - - +
84A GLY* 3.2 45.1 - - - +
85A GLU 3.4 8.1 - - - +
86A PRO* 4.6 1.1 - - + -
125A LYS* 6.0 5.8 - - + -
126A ILE 3.9 7.7 + - - +
127A GLU* 3.5 35.3 - - + +
128A ARG* 2.9 27.7 + - - +
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Residues in contact with LYS 82 (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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80A SER 3.4 0.2 + - - -
81A LEU* 1.3 75.5 - - - +
83A ASP* 1.3 90.4 + - - +
84A GLY 3.1 1.1 + - - -
85A GLU* 2.9 22.0 + - - +
87A PHE* 3.6 57.0 - - + +
127A GLU* 4.9 0.4 - - - -
128A ARG* 3.9 21.1 - - + +
136A ALA* 3.6 28.2 - - + +
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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