Contacts of the helix formed by residues 79 - 95 (chain D) in PDB entry 3SRF
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 THR 79 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78D GLY* 1.3 75.2 - - - -
80D HIS* 1.3 66.6 + - - +
81D GLU* 3.7 14.1 + - - +
82D TYR* 3.3 27.7 + - - +
83D HIS* 3.2 19.4 + - - -
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Residues in contact with HIS 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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75D PHE* 4.7 4.3 - + - -
79D THR* 1.3 77.4 - - - +
81D GLU* 1.3 61.5 + - - +
83D HIS* 3.6 3.3 + - - +
84D ALA* 3.2 19.9 + - - +
223D LYS* 5.4 3.3 + - - -
226D GLN* 3.6 18.2 - - + +
227D ASP* 3.0 29.4 + - - -
230D PHE* 3.2 63.5 - + + -
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Residues in contact with GLU 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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79D THR* 3.2 11.7 + - - +
80D HIS* 1.3 77.0 - - - +
82D TYR* 1.3 63.6 + - - +
84D ALA* 3.6 7.3 + - - +
85D GLU* 3.4 19.9 + - - +
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Residues in contact with TYR 82 (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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50D ILE 5.8 3.4 - - - -
51D GLY* 4.6 3.0 - - - -
52D PRO* 4.3 22.7 - - - +
55D ARG* 3.0 70.2 + - - +
78D GLY* 4.8 8.5 - - - -
79D THR* 3.3 23.9 + - - +
81D GLU* 1.3 80.2 + - - +
83D HIS* 1.3 81.6 + + - +
85D GLU* 3.2 3.1 + - - -
86D THR* 3.2 19.2 + - - -
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Residues in contact with HIS 83 (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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73D LEU* 3.7 19.3 - - + +
74D ASN 3.1 31.2 + - - -
75D PHE* 3.6 44.9 - + + -
77D HIS 2.8 24.2 + - - -
78D GLY* 4.0 5.9 + - - -
79D THR 3.2 23.8 + - - +
80D HIS 4.2 3.6 - - - +
81D GLU 3.4 0.2 - - - -
82D TYR* 1.3 90.9 - + - +
84D ALA* 1.3 64.8 + - - +
86D THR* 3.2 5.8 + - - +
87D ILE* 3.0 31.0 + - - +
230D PHE* 4.2 2.9 - - + -
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Residues in contact with ALA 84 (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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80D HIS 3.2 18.8 + - - +
81D GLU* 3.6 8.5 - - - +
82D TYR 3.3 0.2 - - - -
83D HIS* 1.3 77.1 - - - +
85D GLU* 1.3 57.0 + - - +
87D ILE* 3.5 3.3 + - - +
88D LYS* 2.9 28.7 + - - +
230D PHE* 4.0 8.6 - - + -
234D GLN* 3.9 29.0 - - - +
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Residues in contact with GLU 85 (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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55D ARG* 3.0 37.8 + - - +
81D GLU 3.4 8.8 + - - +
82D TYR* 3.2 3.5 + - - +
84D ALA* 1.3 75.9 - - - +
86D THR* 1.3 60.7 + - - +
88D LYS* 3.3 17.2 - - + +
89D ASN* 2.8 44.5 + - - +
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Residues in contact with THR 86 (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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50D ILE* 3.7 33.9 - - + +
55D ARG* 3.2 28.8 + - + +
73D LEU* 3.8 26.5 - - + -
82D TYR* 3.2 17.9 + - - -
83D HIS* 3.2 9.8 + - - +
85D GLU* 1.3 74.5 - - - +
87D ILE* 1.3 58.9 + - - +
89D ASN* 3.1 7.2 + - - +
90D VAL* 2.8 34.2 + - + +
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Residues in contact with ILE 87 (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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73D LEU* 3.5 19.7 - - + -
75D PHE* 5.5 2.5 - - + -
83D HIS 3.0 19.4 + - - +
84D ALA 3.9 3.8 - - - +
86D THR* 1.3 75.1 - - - +
88D LYS* 1.3 62.1 + - - +
90D VAL* 3.5 7.9 + - - +
91D ARG* 3.1 68.6 + - - +
109D VAL* 4.1 25.4 - - + -
111D LEU* 6.3 0.7 - - + -
230D PHE* 4.5 8.1 - - + -
234D GLN* 4.0 32.1 - - + +
236D VAL* 4.6 7.4 - - + -
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Residues in contact with LYS 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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84D ALA 2.9 19.0 + - - +
85D GLU* 3.3 18.6 - - + +
86D THR 3.2 0.2 - - - -
87D ILE* 1.3 77.3 - - - +
89D ASN* 1.3 61.4 + - - +
91D ARG* 3.4 7.5 + - - +
92D THR* 2.5 44.4 + - - +
234D GLN* 5.5 0.4 + - - -
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Residues in contact with ASN 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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55D ARG* 3.1 38.6 + - - +
56D SER* 4.2 2.4 - - - +
57D VAL* 3.4 26.9 - - + +
60D LEU* 3.7 6.5 - - + +
85D GLU* 2.8 38.5 + - - +
86D THR 3.5 4.9 - - - +
88D LYS* 1.3 81.1 + - - +
90D VAL* 1.3 65.4 + - - +
92D THR* 3.1 6.7 + - - -
93D ALA* 3.0 25.1 + - - +
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Residues in contact with VAL 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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50D ILE* 4.5 1.6 - - + -
60D LEU* 3.5 23.8 - - + +
64D ILE* 4.6 1.5 - - + +
68D MET* 5.3 3.1 - - + -
71D ALA* 3.9 25.6 - - + -
73D LEU* 4.9 3.4 - - + -
86D THR* 2.8 36.4 + - + +
87D ILE* 3.7 8.5 - - - +
89D ASN* 1.3 72.7 - - - +
91D ARG* 1.3 55.3 + - + +
93D ALA* 3.4 2.6 + - - +
94D THR* 2.6 36.2 + - - +
107D VAL* 3.8 27.8 - - + +
109D VAL* 4.2 15.7 - - + -
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Residues in contact with ARG 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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87D ILE* 3.1 43.7 + - + +
88D LYS* 3.7 6.0 - - - +
90D VAL* 1.3 75.3 - - + +
92D THR* 1.3 60.7 + - - +
94D THR* 4.1 6.1 - - - -
95D GLU* 2.8 41.8 + - + +
109D VAL* 4.4 15.1 - - + +
234D GLN* 2.7 35.9 + - - -
235D ASP* 2.8 26.2 + - - +
236D VAL* 4.7 0.8 - - - +
237D ASP* 5.7 0.6 + - - -
460D ARG* 5.9 6.9 - - - +
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Residues in contact with THR 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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57D VAL* 4.3 19.8 - - + +
61D LYS* 5.2 0.3 - - - -
88D LYS* 2.5 36.0 + - - +
89D ASN* 3.5 10.1 + - - -
91D ARG* 1.3 75.1 - - - +
93D ALA* 1.3 61.1 + - - +
95D GLU* 3.7 4.0 + - - +
96D SER* 3.3 21.1 + - - -
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Residues in contact with ALA 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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57D VAL* 3.9 9.8 - - + +
60D LEU* 3.8 23.1 - - + -
61D LYS* 3.8 24.5 - - + +
64D ILE* 4.0 5.8 - - + -
89D ASN 3.0 15.3 + - - +
90D VAL 3.7 4.3 - - - +
92D THR* 1.3 75.7 - - - +
94D THR* 1.3 61.8 + - - +
96D SER* 2.7 26.3 + - - -
97D PHE* 3.3 10.9 - - - -
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Residues in contact with THR 94 (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 ILE* 3.7 12.2 - - + +
90D VAL* 2.6 25.1 + - - +
91D ARG* 3.2 7.3 + - - -
93D ALA* 1.3 74.7 - - - +
95D GLU* 1.3 63.5 + - - +
96D SER 3.2 1.3 + - - -
97D PHE* 3.4 14.3 + - - +
104D TYR* 3.3 33.2 - - + +
105D ARG 3.6 23.5 - - - +
107D VAL* 3.5 37.3 + - + +
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Residues in contact with GLU 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 ARG* 2.8 25.1 + - + +
92D THR* 4.0 4.9 - - - +
94D THR* 1.3 74.5 - - - +
96D SER* 1.3 59.2 + - - +
97D PHE 3.1 6.1 - - - -
98D ALA* 3.3 34.5 + - + +
99D SER 4.8 0.5 + - - -
104D TYR* 2.6 29.2 + - - -
474D LYS* 5.2 4.7 + - - -
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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