Contacts of the strand formed by residues 73 - 78 (chain B) in PDB entry 6DWM
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 73 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B PRO* 4.1 13.0 - - + -
41B PRO* 3.4 23.4 - - - +
70B TYR 4.2 3.5 - - - +
71B GLY 3.3 0.6 - - - -
72B ASP* 1.3 83.8 - - + +
74B LEU* 1.3 61.8 + - - +
84B VAL* 4.1 20.0 - - + -
85B VAL 3.9 2.0 - - - -
86B LEU* 4.2 4.5 - - + -
91B THR* 3.7 21.8 - - + -
396B LEU* 4.1 17.5 - - + +
397B LYS* 4.5 4.5 - - + -
399B PHE* 3.8 36.0 - - + -
401B ILE* 4.7 8.1 - - + -
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Residues in contact with LEU 74 (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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40B PRO* 4.2 4.5 - - - -
41B PRO 3.2 12.8 - - - +
42B GLY* 5.0 0.9 - - - -
43B PRO* 5.7 0.4 - - + -
63B LEU* 4.6 4.7 - - + +
66B MET* 4.0 21.1 - - + +
67B SER* 3.6 37.9 - - - +
70B TYR* 4.1 14.1 - - + -
71B GLY 3.7 8.7 - - - +
73B VAL* 1.3 75.2 - - - +
75B GLN* 1.3 63.5 + - - +
76B ILE* 4.0 21.5 - - + -
84B VAL* 3.3 8.1 - - - +
85B VAL* 2.9 55.2 + - + +
87B SER* 5.0 1.6 - - - +
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Residues in contact with GLN 75 (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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39B ASN* 4.7 5.2 - - - +
40B PRO* 3.4 44.0 - - + +
41B PRO 2.8 7.1 + - - +
42B GLY* 3.6 18.6 - - - -
43B PRO* 4.1 2.4 - - - +
51B HIS* 4.8 1.2 - - - -
74B LEU* 1.3 75.5 - - - +
76B ILE* 1.3 78.3 + - - +
77B ARG* 6.0 0.9 - - + +
82B PRO* 3.8 22.2 - - + +
83B VAL 3.4 11.9 - - - +
84B VAL* 4.6 4.3 - - + -
405B ARG* 4.2 15.0 - - - +
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Residues in contact with ILE 76 (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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43B PRO* 4.8 0.4 - - + -
51B HIS* 3.6 25.6 - - + +
55B LEU* 4.3 23.3 - - + -
63B LEU* 4.1 13.0 - - + -
66B MET* 3.7 30.1 - - + -
74B LEU* 4.0 7.6 - - + -
75B GLN* 1.3 85.7 - - - +
77B ARG* 1.3 67.4 + - - +
78B ILE* 4.5 7.6 - - + -
82B PRO* 3.3 5.7 - - - +
83B VAL* 2.8 48.5 + - + +
85B VAL* 4.0 20.0 - - + -
408B PHE* 5.0 1.3 - - + -
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Residues in contact with ARG 77 (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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43B PRO 5.7 0.8 + - - -
45B GLY* 3.2 27.5 + - - +
46B TRP 3.1 27.7 + - - -
47B PRO* 4.2 9.6 + - - +
50B GLY* 4.0 5.1 - - - -
51B HIS* 2.7 47.0 + - - +
75B GLN* 6.0 0.9 - - + +
76B ILE* 1.3 81.9 - - - +
78B ILE* 1.3 63.4 + - - +
79B GLY 3.9 17.0 + - - +
80B SER* 4.5 12.8 - - - +
81B THR 3.2 12.6 - - - +
82B PRO* 4.1 12.1 - - + -
83B VAL 4.7 0.2 - - - +
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Residues in contact with ILE 78 (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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49B ILE 4.1 2.0 - - - -
52B MET* 4.3 23.8 - - + +
55B LEU* 3.8 30.3 - - + -
76B ILE* 4.5 4.9 - - + -
77B ARG* 1.3 75.7 - - - +
79B GLY* 1.3 64.6 + - - +
80B SER 3.3 0.2 + - - -
81B THR* 3.0 21.1 + - - +
83B VAL* 4.5 7.9 - - + -
231B GLY* 3.9 26.7 - - - +
233B PRO* 5.0 3.1 - - + -
236B PHE* 3.3 50.8 - - + +
237B ILE* 5.4 0.2 - - + -
408B PHE* 4.0 15.7 - - + -
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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