Contacts of the helix formed by residues 87 - 96 (chain D) in PDB entry 3CWT
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 87 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A TYR* 5.3 3.5 + - - +
7D GLN* 3.4 25.0 + - - +
85D GLN* 3.5 2.9 + - - +
86D CYS* 1.3 76.1 - - - +
88D PRO* 1.3 62.6 - - - +
89D GLN* 3.0 33.2 + - - +
90D ILE* 2.9 41.8 + - + +
91D VAL* 3.5 10.5 + - - +
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Residues in contact with PRO 88 (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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7D GLN* 3.9 6.5 - - + +
8D PRO 3.5 24.9 - - - +
9D PRO* 3.7 10.8 - - + +
86D CYS* 3.1 24.7 - - - +
87D ASN* 1.3 83.3 - - - +
89D GLN* 1.3 61.5 + - - +
91D VAL* 4.5 4.5 - - + +
92D ASN* 2.8 46.0 + - - +
103D PRO 3.8 13.2 - - - +
105D LEU 5.8 0.9 - - - +
106D ARG* 3.6 23.8 - - - +
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Residues in contact with GLN 89 (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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8D PRO 5.5 0.2 + - - -
9D PRO* 5.7 0.8 - - - +
87D ASN* 3.0 21.1 + - - +
88D PRO* 1.3 80.1 - - - +
90D ILE* 1.3 62.1 + - + +
92D ASN* 4.7 2.2 - - - +
93D GLY* 3.2 22.3 + - - -
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Residues in contact with ILE 90 (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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87D ASN* 2.9 36.5 + - + +
89D GLN* 1.3 85.9 - - + +
91D VAL* 1.3 65.8 + - + +
93D GLY* 3.4 1.8 + - - -
94D ALA* 3.2 21.5 + - - +
263D TRP* 3.8 29.4 - - + +
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Residues in contact with VAL 91 (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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86D CYS* 4.1 14.4 - - - -
87D ASN 3.9 11.4 - - - +
88D PRO* 3.3 7.5 + - + +
90D ILE* 1.3 76.1 - - + +
92D ASN* 1.3 57.3 + - - +
94D ALA* 3.0 5.2 + - - +
95D LEU* 2.7 56.2 + - + +
263D TRP* 4.2 23.3 - - + -
266D TYR* 3.9 42.2 - - + -
270D HIS* 5.5 2.5 - - + -
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Residues in contact with ASN 92 (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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9D PRO* 5.4 1.0 - - - +
88D PRO* 2.8 28.3 + - - +
89D GLN* 4.7 1.8 - - - +
91D VAL* 1.3 77.8 - - - +
93D GLY* 1.3 61.8 + - - +
94D ALA 3.0 2.2 - - - -
95D LEU* 4.2 5.4 - - - +
96D GLY* 2.9 34.3 + - - +
99D GLY* 3.8 23.9 - - - +
100D ALA* 6.2 0.7 - - - -
103D PRO* 3.3 39.1 + - + +
270D HIS* 4.6 6.1 - - - -
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Residues in contact with GLY 93 (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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89D GLN 3.2 19.6 + - - -
90D ILE* 3.9 2.7 - - - -
91D VAL 3.3 0.4 - - - -
92D ASN* 1.3 78.2 - - - +
94D ALA* 1.3 57.9 + - - +
96D GLY* 4.4 3.3 + - - -
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Residues in contact with ALA 94 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90D ILE 3.2 11.6 + - - +
91D VAL 3.0 7.3 + - - +
92D ASN 3.0 0.2 - - - -
93D GLY* 1.3 77.8 - - - +
95D LEU* 1.3 64.7 + - + +
96D GLY* 3.2 2.3 + - - -
259D ARG 5.5 3.1 - - - +
260D TRP* 5.5 1.6 - - - +
261D LYS 5.9 1.6 - - - +
262D PRO* 5.7 3.4 - - + -
263D TRP* 3.6 23.8 - - + +
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Residues in contact with LEU 95 (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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91D VAL* 2.7 40.9 + - + +
92D ASN* 4.5 4.7 - - - +
94D ALA* 1.3 73.6 - - + +
96D GLY* 1.3 63.8 + - - +
97D ARG 3.4 1.7 + - - -
98D LEU* 3.4 17.1 + - + +
99D GLY* 4.4 11.2 - - - +
260D TRP* 3.5 53.2 + - + +
263D TRP* 4.4 8.5 - - + +
266D TYR* 4.0 4.9 - - + -
267D ALA* 3.9 29.2 - - + +
270D HIS* 4.1 15.7 - - + +
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Residues in contact with GLY 96 (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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92D ASN* 2.9 22.0 + - - +
93D GLY 5.0 3.1 - - - -
94D ALA 3.2 4.0 - - - +
95D LEU* 1.3 76.0 - - - +
97D ARG* 1.3 62.0 + - - -
98D LEU 3.3 1.0 + - - -
99D GLY* 3.3 10.4 + - - -
100D ALA* 3.5 8.9 + - - +
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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