Contacts of the helix formed by residues 86 - 96 (chain A) in PDB entry 3D4S
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 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A VAL 3.9 5.8 - - - +
82A MET* 3.2 23.7 + - - +
84A LEU 3.8 0.4 - - - -
85A ALA* 1.3 82.0 - - - +
87A VAL* 1.3 68.4 + - - +
88A PRO* 3.4 1.1 - - - -
89A PHE 3.4 1.7 + - - -
90A GLY* 3.0 10.7 + - - -
109A TRP* 2.9 28.1 + - - +
112A ILE* 3.7 26.7 - - + -
113A ASP* 3.6 43.7 - - + +
116A CYS* 4.9 0.2 - - - -
316A TYR* 3.7 19.5 - - + +
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A MET 4.7 1.1 - - - +
43A ILE* 4.6 9.6 - - + -
44A VAL* 3.5 22.9 - - + -
47A ILE* 4.3 14.8 - - + -
82A MET* 2.8 27.5 + - + +
83A GLY* 4.6 2.5 - - - -
86A VAL* 1.3 71.4 - - - +
88A PRO* 1.4 61.5 - - + +
90A GLY* 3.1 2.4 + - - +
91A ALA* 2.8 28.6 + - - +
313A TRP* 3.7 28.1 - - + -
316A TYR* 3.9 34.5 - - + -
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Residues in contact with PRO 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 4.0 19.5 - - + -
83A GLY 3.3 26.7 - - - +
84A LEU* 3.5 16.4 - - - +
85A ALA 4.3 0.2 - - - -
86A VAL 3.5 12.3 - - - +
87A VAL* 1.4 89.7 - - + +
89A PHE* 1.3 62.6 + - + +
91A ALA* 3.5 5.7 + - + +
92A ALA* 3.2 24.4 + - - +
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Residues in contact with PHE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU 4.3 6.5 - - - -
85A ALA* 3.3 31.0 - - - -
86A VAL 3.4 0.6 + - - -
87A VAL 3.3 0.4 - - - -
88A PRO* 1.3 80.1 - - + +
90A GLY* 1.3 60.9 + - - +
92A ALA* 3.7 6.8 - - - +
93A HIS* 3.1 27.4 + - - +
99A TRP* 3.4 16.1 - - + -
101A PHE* 3.6 37.9 - + - -
105A TRP* 3.3 38.8 - + - -
109A TRP* 3.7 16.8 - - + +
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Residues in contact with GLY 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A VAL 3.0 11.5 + - - -
87A VAL* 3.1 4.5 + - - -
89A PHE* 1.3 77.8 - - - +
91A ALA* 1.3 60.4 + - - +
93A HIS* 3.4 6.8 + - - +
94A ILE* 3.2 28.1 + - - +
109A TRP* 3.7 21.7 - - - +
313A TRP* 4.0 11.9 - - - -
316A TYR* 5.7 3.6 - - - -
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A MET* 3.7 37.2 - - + +
44A VAL* 5.6 1.1 - - + -
87A VAL* 2.8 17.3 + - + +
88A PRO* 3.7 8.1 - - + +
90A GLY* 1.3 75.4 - - - +
92A ALA* 1.3 62.6 + - - +
94A ILE* 3.5 2.3 + - - +
95A LEU* 3.2 34.5 + - + +
313A TRP* 3.8 7.5 - - + -
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Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A PRO 3.2 17.0 + - - +
89A PHE 3.7 6.1 - - - +
90A GLY 3.3 0.2 - - - -
91A ALA* 1.3 78.2 - - - +
93A HIS* 1.3 59.9 - - - +
95A LEU* 5.2 1.6 - - - -
96A MET* 3.2 45.1 + - - +
98A MET 4.6 0.9 - - - -
101A PHE* 3.8 27.1 - - + -
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Residues in contact with HIS 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A PHE 3.1 18.0 + - - +
90A GLY* 3.6 8.9 + - - +
91A ALA 3.3 0.4 - - - -
92A ALA* 1.3 77.6 - - - +
94A ILE* 1.3 61.8 + - - +
97A LYS* 3.2 24.8 + - - -
98A MET* 3.5 27.5 + - - -
99A TRP* 3.7 32.0 - + + -
101A PHE* 5.7 0.2 - - - -
109A TRP* 5.1 8.9 - + + -
191A CYS* 4.1 20.1 + - + -
192A ASP* 3.8 23.7 + - - -
305A LYS* 5.6 2.9 - - - -
309A ILE* 5.6 10.5 - - + +
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Residues in contact with ILE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TRP* 6.3 1.8 - - + -
36A MET* 5.0 6.5 - - - -
40A MET* 4.0 19.7 - - + -
90A GLY 3.2 14.1 + - - +
91A ALA 3.9 4.5 - - - +
92A ALA 3.3 0.4 - - - -
93A HIS* 1.3 82.4 - - - +
95A LEU* 1.3 72.0 + - + +
97A LYS* 3.3 23.9 + - - +
309A ILE* 3.9 24.5 - - + -
313A TRP* 3.3 39.7 - - + +
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Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TRP* 5.4 5.6 - - + -
33A VAL* 3.9 43.7 - - + +
36A MET* 4.6 20.0 - - + -
37A GLY* 3.9 28.0 - - - +
40A MET* 4.6 11.0 - - + -
91A ALA* 3.2 21.0 + - + +
92A ALA* 4.6 2.2 - - - +
94A ILE* 1.3 83.0 - - + +
96A MET* 1.3 64.1 - - + +
97A LYS* 4.3 12.4 + - - +
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Residues in contact with MET 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ALA* 3.2 34.7 + - - +
95A LEU* 1.3 78.6 - - + +
97A LYS* 1.3 68.0 + - - +
98A MET* 3.2 25.3 + - + +
100A THR* 3.4 41.5 - - + +
101A PHE* 5.5 1.8 - - - -
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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