Contacts of the strand formed by residues 81 - 94 (chain D) in PDB entry 1S4Y
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 CYS 81 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D CYS* 2.1 51.8 - - - -
12D CYS 3.8 1.3 - - - -
40D CYS* 3.8 23.3 - - - +
41D GLU* 3.6 17.7 - - - -
42D GLY 3.5 23.2 + - - +
44D CYS* 3.2 11.3 - - - +
80D CYS* 1.3 71.3 - - - +
82D VAL* 1.3 66.4 + - - +
83D PRO* 4.8 0.2 - - - +
114D GLY 3.6 0.2 - - - -
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Residues in contact with VAL 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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82B VAL* 4.3 17.5 - - + -
83B PRO* 6.1 0.2 - - + -
116B SER* 3.8 31.2 - - - +
40D CYS* 3.5 7.6 - - - -
80D CYS* 3.9 20.6 - - + +
81D CYS* 1.3 81.4 - - - +
83D PRO* 1.3 84.5 - - + +
84D THR* 3.1 5.5 + - + +
113D CYS* 3.5 0.2 - - - -
114D GLY 3.0 38.0 + - - +
116D SER* 4.4 15.3 - - - +
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Residues in contact with PRO 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B HIS* 5.9 2.2 - - + -
116B SER* 5.9 2.5 - - - -
40D CYS* 3.6 16.6 - - + -
82D VAL* 1.3 95.7 - - + +
84D THR* 1.3 63.9 + - - +
86D LEU* 3.8 32.0 - - + +
110D VAL* 3.8 22.7 - - + -
112D GLU 3.4 8.5 - - - +
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Residues in contact with THR 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ASN* 5.4 6.2 + - - +
82D VAL* 3.1 17.2 + - + +
83D PRO* 1.3 75.5 - - - +
85D LYS* 1.3 61.0 + - - +
86D LEU* 4.3 3.3 - - - +
112D GLU* 2.8 26.5 + - - +
113D CYS 3.4 6.9 + - - -
114D GLY* 3.6 21.1 - - - +
115D CYS 5.5 2.7 - - - +
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Residues in contact with LYS 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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33C LYS* 4.9 6.0 - - - +
83D PRO 3.5 0.8 - - - -
84D THR* 1.3 81.2 - - - +
86D LEU* 1.3 72.7 + - - +
110D VAL* 3.9 0.5 - - - +
111D GLU* 2.5 61.6 + - - +
112D GLU* 3.2 40.0 + - + +
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Residues in contact with LEU 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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59B HIS* 5.8 1.6 - - + -
83D PRO* 3.8 31.2 - - + +
84D THR 4.3 1.6 - - - -
85D LYS* 1.3 97.9 - - - +
87D ARG* 1.3 61.1 - - - +
88D PRO* 4.3 2.9 - - - +
106D GLN* 5.6 0.9 - - - +
107D ASN* 3.5 53.2 - - + +
109D ILE 3.3 9.2 - - - +
110D VAL* 4.3 13.9 - - + +
111D GLU* 3.8 7.0 - - - +
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Residues in contact with ARG 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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29C GLY* 5.9 3.8 - - - -
30C GLU 6.0 0.8 - - - +
33C LYS* 3.6 39.5 - - - +
34C ARG 5.0 0.4 + - - -
57C LEU* 4.1 13.9 - - - +
58C ASP* 3.2 54.1 + - - +
86D LEU* 1.3 71.8 - - - +
88D PRO* 1.3 109.9 + - + +
89D MET* 4.7 1.4 - - - +
107D ASN 4.5 2.7 - - - -
108D MET 3.1 21.7 + - - -
109D ILE* 3.0 36.7 + - + +
111D GLU* 2.5 28.4 + - - +
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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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57C LEU* 3.6 24.0 - - + -
86D LEU 4.3 2.9 - - - +
87D ARG* 1.3 130.1 + - - +
89D MET* 1.3 63.1 + - - +
104D ASP* 5.4 0.7 - - + -
105D ILE 3.1 14.8 - - - +
106D GLN* 3.3 34.5 - - - +
109D ILE* 4.8 1.7 - - - +
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Residues in contact with MET 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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57C LEU* 3.8 6.9 - - - +
58C ASP 5.8 3.6 - - - +
59C ASP* 6.4 1.8 - - - -
20D PHE* 4.5 0.2 - - + -
32D PRO* 4.0 19.5 - - + -
35D TYR* 3.5 50.5 - - + -
87D ARG* 4.7 2.5 - - - +
88D PRO* 1.3 76.9 - - - +
90D SER* 1.3 67.1 + - - +
91D MET* 3.8 18.8 + - + +
103D LYS 3.7 0.5 - - - +
105D ILE* 2.8 40.4 + - - +
108D MET* 3.2 41.3 - - + -
109D ILE* 4.4 13.0 - - + -
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Residues in contact with SER 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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56C TRP* 3.4 46.7 - - - +
57C LEU* 3.0 28.0 + - - +
32D PRO* 4.0 6.1 - - - +
89D MET* 1.3 83.0 - - - +
91D MET* 1.3 63.4 - - - +
102D LYS* 3.5 4.6 - - - -
103D LYS 3.4 5.4 - - - -
104D ASP* 2.6 21.9 + - - -
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Residues in contact with MET 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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58B PHE* 3.8 30.5 - - + -
56C TRP* 3.9 4.5 - - - -
20D PHE* 4.3 9.2 - - - -
28D TRP* 4.0 15.9 - - + -
29D ILE* 4.2 17.0 - - + -
31D ALA 3.4 8.5 - - - +
89D MET* 3.9 14.8 - - + +
90D SER* 1.3 79.5 - - - +
92D LEU* 1.3 58.4 + - - +
93D TYR* 3.5 36.3 - - + -
101D ILE 3.6 0.9 - - - +
102D LYS* 3.2 5.5 - - - +
103D LYS 2.9 32.2 + - - +
105D ILE* 3.7 26.0 - - + -
108D MET* 4.2 4.0 - - + -
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Residues in contact with LEU 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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38C TYR* 4.6 6.7 - - + +
40C SER* 3.6 34.1 - - - +
52C LYS* 4.7 2.9 - - + -
56C TRP* 3.9 8.0 - - + -
77C VAL* 4.8 1.3 - - + -
79C PHE* 3.9 18.8 - - + -
29D ILE* 3.9 2.3 - - - +
30D ILE* 3.1 45.4 + - + -
31D ALA* 3.0 23.9 + - + +
91D MET* 1.3 70.0 - - - +
93D TYR* 1.3 63.8 + - - +
100D ILE* 3.4 25.1 - - + -
101D ILE 3.3 8.7 - - - +
102D LYS* 4.0 17.0 - - + -
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Residues in contact with TYR 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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28D TRP* 3.1 46.2 - + + +
29D ILE* 4.0 4.9 - - - -
30D ILE* 3.8 9.0 - - - -
91D MET* 3.5 42.4 - - + -
92D LEU* 1.3 76.1 - - - +
94D TYR* 1.3 66.8 + - - +
95D ASP* 3.8 9.1 + - + -
100D ILE* 3.4 2.5 - - - -
101D ILE* 2.8 51.9 + - + +
103D LYS* 3.2 38.3 - - + +
105D ILE* 4.9 5.1 - - + +
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Residues in contact with TYR 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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42C ARG* 3.7 22.9 + - - -
76C GLN* 5.0 6.8 - - - +
77C VAL* 3.3 26.3 - - + +
27D ASP 3.5 24.0 - - - -
28D TRP* 2.7 38.6 + - + +
30D ILE* 4.0 17.3 - - + -
93D TYR* 1.3 79.9 - - - +
95D ASP* 1.3 68.5 + - - +
98D GLN* 3.8 36.8 - - + +
99D ASN 3.2 5.4 - - - +
100D ILE* 3.8 14.1 - - + -
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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