Contacts of the strand formed by residues 44 - 52 (chain B) in PDB entry 3DIF
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 GLY 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A TYR* 4.4 16.6 - - - -
99A GLY 5.3 2.2 - - - -
100A GLY* 5.2 7.4 - - - -
38B LYS 3.5 1.4 - - - +
39B GLN* 2.7 30.9 + - - -
40B ARG 3.2 18.7 + - - -
41B PRO 4.9 1.8 + - - -
42B GLY 3.7 1.0 - - - -
43B GLN* 1.3 78.7 - - - +
45B LEU* 1.3 58.9 + - - -
46B GLU* 5.5 1.1 - - - +
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Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 5.8 1.1 - - + -
44A PRO* 4.3 25.4 - - + -
87A TYR* 3.7 42.4 - - + -
98A PHE* 3.3 54.9 + - + +
99A GLY 5.0 1.0 + - - -
37B VAL* 3.8 21.1 - - + -
38B LYS 3.4 0.9 - - - -
39B GLN* 3.7 33.4 - - + +
43B GLN 3.9 1.8 + - - +
44B GLY* 1.3 73.0 - - - -
46B GLU* 1.3 65.8 + - - +
95B PHE* 4.9 3.1 - - + -
109B TRP* 4.8 1.1 - - + -
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Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A THR* 6.5 0.2 - - - +
98A PHE* 4.5 1.3 - - - -
37B VAL* 3.2 7.1 - - - +
38B LYS* 2.7 55.4 + - + +
40B ARG* 3.4 25.6 + - - -
43B GLN* 4.1 14.9 - - - +
44B GLY 5.5 1.0 - - - +
45B LEU* 1.3 80.9 - - - +
47B TRP* 1.3 61.6 + - - +
48B ILE* 3.6 0.7 + - - +
61B ASN* 5.3 2.4 + - - +
63B LYS* 3.3 38.0 + - - +
64B PHE* 4.2 14.8 - - + -
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Residues in contact with TRP 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A THR* 3.1 27.6 - - - -
95A PRO* 3.6 25.6 - - + -
96A TRP* 3.5 49.6 + + - +
97A THR* 6.0 0.2 - - - +
98A PHE* 4.2 10.0 - - + -
35B HIS* 3.4 19.1 + - + -
36B TRP 3.7 15.9 - - - -
37B VAL* 4.4 3.1 - - + -
46B GLU* 1.3 71.2 - - - +
48B ILE* 1.3 56.8 + - - +
49B GLY* 3.4 28.4 + - - -
50B TRP* 3.7 12.3 - + - -
59B LYS* 4.4 9.9 - - + -
60B TYR 4.2 4.9 - - - -
61B ASN* 2.7 54.6 + - + +
64B PHE* 4.1 1.1 - - - -
106B PHE* 3.7 26.2 - + + -
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Residues in contact with ILE 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B TRP* 2.8 20.2 + - + +
37B VAL 4.2 4.3 - - - +
38B LYS* 3.8 12.1 - - + +
46B GLU 4.0 7.2 - - - +
47B TRP* 1.3 76.3 - - - +
49B GLY* 1.3 58.1 + - - +
60B TYR* 3.6 6.5 - - + +
61B ASN* 2.8 27.2 + - - +
64B PHE* 3.8 34.8 - - + +
68B ALA* 3.8 29.6 - - + -
70B LEU* 5.0 2.9 - - + -
81B MET* 3.8 18.6 - - + -
83B LEU* 5.4 1.1 - - + -
94B TYR* 3.7 36.3 - - + -
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Residues in contact with GLY 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B HIS* 3.4 2.3 - - - -
36B TRP 2.9 24.9 + - - -
47B TRP* 3.4 20.9 + - - +
48B ILE* 1.3 82.5 - - - +
50B TRP* 1.3 59.5 + - - -
59B LYS 3.0 14.8 - - - -
60B TYR* 4.1 0.7 - - - -
70B LEU* 3.5 14.9 - - - +
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Residues in contact with TRP 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A TRP* 4.1 11.0 - + - -
33B TYR* 3.5 54.6 - + + -
34B ILE 3.2 15.0 - - - +
35B HIS* 3.5 33.4 - + + +
47B TRP* 3.7 15.0 - + - -
49B GLY* 1.3 73.0 - - - -
51B VAL* 1.3 65.0 + - - +
52B PHE* 4.0 3.8 - + + -
57B ASN* 3.5 29.6 - - + -
58B THR* 3.4 19.1 + - - -
59B LYS* 2.9 63.5 + - + +
70B LEU* 3.6 8.9 - - - +
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B TYR* 3.4 2.8 - - - -
34B ILE* 2.9 49.0 + - + +
36B TRP* 5.0 2.5 - - - +
50B TRP* 1.3 79.1 - - - +
52B PHE* 1.3 66.1 + - - +
53B PRO* 3.4 2.8 - - + +
56B GLY* 4.3 11.7 - - - +
57B ASN 3.3 11.2 - - - +
58B THR* 4.5 0.4 - - - +
70B LEU* 4.2 19.1 - - + +
71B THR* 4.0 27.6 - - - +
72B ALA* 4.1 13.2 - - + +
79B ALA* 4.2 15.9 - - + -
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Residues in contact with PHE 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B THR 3.1 25.4 - - - -
31B SER* 3.9 10.8 - - - -
32B TYR 3.8 15.0 - - - -
33B TYR* 3.4 37.2 - + + -
50B TRP* 3.8 0.6 - + + -
51B VAL* 1.3 72.6 - - - +
53B PRO* 1.3 72.1 - - + +
55B SER* 3.4 8.9 + - - +
56B GLY* 2.9 26.0 + - - -
57B ASN* 2.7 34.4 + - + +
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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