Contacts of the strand formed by residues 49 - 55 (chain B) in PDB entry 4DDI
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 VAL 49 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B THR* 4.9 10.5 - - + -
37B ILE 3.9 3.4 - - - +
38B MET* 4.0 24.9 - - + -
47B GLY 4.9 1.3 - - - +
48B GLY* 1.3 77.4 - - - +
50B PHE* 1.3 65.4 - - - +
51B PHE* 3.9 39.1 + - + -
71B THR* 4.2 4.7 + - - +
146B ALA* 3.6 29.3 + - - +
1025B ALA* 5.0 7.0 - - + +
1026B TYR* 4.4 27.3 - - + -
1029B ALA* 4.5 12.6 - - + -
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Residues in contact with PHE 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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35B ALA 3.6 1.0 - - - +
37B ILE* 2.9 52.0 + - + +
39B GLY* 4.3 5.8 - - - -
45B TYR* 3.8 38.1 - + + -
48B GLY 3.9 9.6 - - - -
49B VAL* 1.3 73.5 - - - +
51B PHE* 1.3 62.6 + - - +
52B LEU* 4.6 1.0 - - - +
69B PHE* 4.1 18.4 - + + -
71B THR* 3.6 20.2 - - + -
72B ARG 4.0 5.8 - - - -
73B ILE* 3.6 44.0 - - + -
110B LEU* 5.3 7.4 - - + -
141B TRP 5.1 2.0 - - - -
142B THR* 4.3 9.4 - - + -
146B ALA* 3.5 20.9 - - + -
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Residues in contact with PHE 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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34B GLN* 3.2 29.4 - - - +
35B ALA 3.4 3.4 - - - -
36B THR* 3.5 26.9 - - + -
49B VAL* 3.9 15.9 - - + -
50B PHE* 1.3 74.2 - - - +
52B LEU* 1.3 65.1 + - - +
69B PHE* 3.7 4.2 - - - +
70B THR* 3.1 26.5 + - - +
71B THR* 3.3 23.8 + - - +
1025B ALA* 3.2 49.4 - - + -
1028B GLU* 4.3 19.1 - - + -
1029B ALA 5.8 0.7 - - - -
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Residues in contact with LEU 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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34B GLN* 3.5 2.7 - - - +
35B ALA* 2.9 59.1 + - + +
37B ILE* 3.6 27.1 - - + -
50B PHE 4.6 0.7 - - - +
51B PHE* 1.3 77.2 - - - +
53B THR* 1.3 63.4 + - - +
54B ILE* 4.5 5.1 - - + +
67B VAL* 3.9 20.4 - - + -
68B ALA 3.1 19.1 - - - +
69B PHE* 3.5 39.7 - - + -
70B THR* 3.6 3.1 - - - -
103B LEU* 5.8 2.7 - - + -
106B ILE* 4.6 10.3 - - + -
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Residues in contact with THR 53 (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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32B HIS* 4.1 20.9 - - + +
33B TRP 3.7 3.1 - - - -
34B GLN* 4.1 15.5 - - + -
52B LEU* 1.3 76.2 - - - +
54B ILE* 1.3 62.4 + - - +
55B HIS* 4.5 11.6 + - - -
66B LYS 3.9 0.7 - - - +
67B VAL* 3.5 2.9 - - - +
68B ALA* 2.9 41.6 + - - +
70B THR* 3.6 28.3 - - + +
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Residues in contact with ILE 54 (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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23B ALA* 4.4 18.4 - - + -
31B PHE 3.5 0.9 - - - +
32B HIS* 3.5 7.4 - - - -
33B TRP* 2.9 52.9 + - + +
35B ALA* 4.5 9.4 - - + -
52B LEU* 4.5 7.4 - - + +
53B THR* 1.3 81.4 - - - +
55B HIS* 1.3 65.6 + - - +
56B PHE* 3.6 24.9 - - + -
65B PRO* 4.1 9.6 - - + -
66B LYS 3.4 8.3 - - - +
67B VAL* 3.9 24.7 - - + -
99B ILE* 4.2 20.0 - - + -
103B LEU* 5.1 2.7 - - + -
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Residues in contact with HIS 55 (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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26A VAL* 4.0 24.8 - - + +
32A HIS* 5.7 5.5 - - - -
31B PHE 3.3 7.9 - - - +
32B HIS* 3.5 40.6 + + + -
53B THR* 4.5 12.7 + - - -
54B ILE* 1.3 79.1 + - - +
56B PHE* 1.3 65.8 + - - +
65B PRO* 3.5 0.9 - - - +
66B LYS* 2.9 64.6 + - + +
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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