Contacts of the strand formed by residues 77 - 81 (chain D) in PDB entry 3SKU
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 ASN 77 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A ARG* 4.3 1.8 - - - +
214A VAL 4.0 0.2 + - - -
215A ASP* 3.0 54.5 + - + +
218A GLY 4.7 2.0 - - - -
219A MET 2.7 25.3 + - - +
220A LEU* 2.8 28.7 - - - +
67D TRP 3.7 4.1 - - - +
68D GLN* 2.9 17.3 + - - +
76D GLN* 1.3 82.6 - - - +
78D VAL* 1.3 63.0 + - - +
80D ILE* 4.3 8.9 - - + +
90D LEU* 4.6 8.7 - - + +
91D ALA 5.5 2.3 - - - +
93D TYR* 4.8 5.0 - - - -
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Residues in contact with VAL 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D TRP* 2.9 23.2 + - + +
68D GLN* 4.3 0.9 - - - -
69D LYS* 4.3 4.5 - - + +
76D GLN* 3.9 8.1 - - + +
77D ASN* 1.3 83.1 - - - +
79D ALA* 1.3 65.9 + - + +
80D ILE* 5.2 0.9 - - - -
88D SER 4.3 0.5 - - - +
89D VAL* 3.5 3.7 - - + +
90D LEU* 2.9 34.8 + - - +
93D TYR* 3.6 52.9 - - + +
97D VAL* 4.9 6.5 - - + -
109D ILE* 4.9 10.5 - - + -
122D TYR* 4.0 17.5 - - + -
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Residues in contact with ALA 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D VAL 3.5 4.0 - - - +
67D TRP* 3.2 35.1 + - + +
78D VAL* 1.3 83.2 - - + +
80D ILE* 1.3 71.5 + - - +
88D SER 3.6 5.2 - - - +
89D VAL* 4.4 11.4 - - + +
97D VAL* 5.1 1.8 - - + -
99D PHE* 3.3 31.0 - - + -
109D ILE* 4.9 4.7 - - + -
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Residues in contact with ILE 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 5.6 6.5 - - + -
132A GLN* 6.4 0.4 - - - +
134A ARG* 5.4 0.7 - - - +
215A ASP* 4.5 7.0 - - - +
220A LEU* 4.1 21.5 - - + -
221A PRO* 4.2 29.8 - - + -
64D GLN* 4.7 5.8 - - - +
65D VAL 3.9 2.5 - - - +
66D THR* 4.5 8.3 - - + -
67D TRP 5.2 0.2 - - - +
77D ASN* 4.3 19.5 - - + +
78D VAL 5.1 0.2 - - - +
79D ALA* 1.3 87.0 - - - +
81D TYR* 1.3 62.4 + - - +
82D ASN* 4.5 8.7 - - + +
87D VAL* 3.1 11.6 - - - +
88D SER* 2.7 48.2 + - - +
90D LEU* 5.0 6.1 - - + -
99D PHE* 3.9 1.7 - - - -
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Residues in contact with TYR 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D GLN* 3.4 20.1 + - - -
65D VAL* 3.6 25.3 + - + +
80D ILE* 1.3 73.0 - - - +
82D ASN* 1.3 59.1 + - - +
83D PRO* 3.0 39.4 - - + +
85D MET 5.4 5.4 - - - -
86D GLY 3.9 6.3 - - - -
87D VAL* 2.8 32.3 - - + -
99D PHE* 4.0 17.0 - - + -
102D PRO* 2.8 53.6 + - + +
103D SER* 4.4 8.7 - - - -
107D GLY* 6.3 0.2 - - - -
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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