Contacts of the strand formed by residues 100 - 115 (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 ILE 100 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13C ASN* 4.5 6.9 - - - +
42C ARG* 3.3 38.6 - - - +
51C VAL* 3.5 31.8 - - + +
52C LYS* 3.5 12.7 + - - -
77C VAL* 3.9 20.0 - - + -
30D ILE* 4.0 10.5 - - + -
92D LEU* 3.4 33.7 - - + -
93D TYR 3.4 2.2 - - - -
94D TYR* 3.8 18.2 - - + -
98D GLN 5.2 0.4 - - - +
99D ASN* 1.3 77.1 - - - +
101D ILE* 1.4 70.3 + - - +
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Residues in contact with ILE 101 (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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13C ASN* 3.6 13.9 - - - +
17C GLU* 3.3 22.7 - - - +
52C LYS* 3.9 2.5 - - - +
91D MET 3.6 1.0 - - - +
92D LEU* 3.3 7.3 - - - +
93D TYR* 2.8 49.0 + - + +
95D ASP* 3.7 36.6 - - + +
99D ASN* 4.1 3.1 - - + +
100D ILE* 1.4 85.3 - - - +
102D LYS* 1.3 64.9 + - - +
103D LYS* 3.3 40.8 - - + -
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Residues in contact with LYS 102 (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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17C GLU* 5.6 0.2 - - - +
25C GLU* 5.6 3.8 + - - -
38C TYR* 3.3 32.5 - - + +
52C LYS* 3.7 17.0 + - + +
55C CYS* 3.1 27.2 + - - +
56C TRP* 3.8 11.4 - - + +
90D SER* 3.5 17.8 + - - -
91D MET 3.2 10.1 - - - +
92D LEU* 4.0 5.6 - - + -
101D ILE* 1.3 76.3 - - - +
103D LYS* 1.3 73.4 + - - +
104D ASP* 2.7 39.8 + - - -
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Residues in contact with LYS 103 (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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17C GLU* 4.8 8.4 + - - -
90D SER* 3.4 1.6 - - - -
91D MET* 2.9 31.7 + - - -
93D TYR* 3.2 31.4 - - + +
101D ILE* 3.3 23.1 - - + -
102D LYS* 1.3 80.8 - - - +
104D ASP* 1.3 66.9 + - - +
105D ILE* 3.6 15.3 + - + +
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Residues in contact with ASP 104 (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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55C CYS 5.9 0.2 - - - -
57C LEU* 3.7 29.6 + - + +
88D PRO* 5.4 0.9 - - + -
89D MET 3.6 3.6 - - - -
90D SER* 2.6 28.4 + - - -
102D LYS* 2.7 25.7 + - - -
103D LYS* 1.3 70.9 - - - +
105D ILE* 1.3 63.1 + - - +
106D GLN* 3.7 7.6 + - - +
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Residues in contact with ILE 105 (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* 4.6 16.2 - - + +
88D PRO* 3.1 5.5 - - - +
89D MET 2.8 40.2 + - - +
91D MET* 3.7 43.5 - - + -
93D TYR* 4.9 4.3 - - + +
103D LYS* 4.1 18.2 - - + +
104D ASP* 1.3 74.8 - - - +
106D GLN* 1.3 75.3 + - - +
108D MET* 3.4 26.6 - - + +
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Residues in contact with GLN 106 (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 LEU 5.6 0.9 - - - +
87D ARG 5.1 0.2 - - - -
88D PRO* 3.3 29.0 - - - +
104D ASP* 3.7 6.9 + - - +
105D ILE* 1.3 87.2 - - - +
107D ASN* 1.3 90.1 + - - +
108D MET* 3.3 1.6 + - - +
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Residues in contact with ASN 107 (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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57B SER* 4.9 3.2 + - - +
59B HIS* 3.6 19.8 + - - +
84B THR 5.6 4.4 + - - -
86D LEU* 3.5 51.1 - - + +
87D ARG 3.9 6.3 + - - -
106D GLN* 1.3 93.2 + - - +
108D MET* 1.3 60.3 + - - +
109D ILE 3.6 1.3 - - - -
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Residues in contact with MET 108 (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* 3.5 50.9 - - + -
59B HIS* 3.3 24.1 - - - -
35D TYR* 3.7 19.7 + - - +
37D ALA* 4.1 0.7 - - - +
87D ARG 3.1 6.9 + - - +
89D MET* 3.2 52.5 - - + -
91D MET* 4.2 11.7 - - + -
105D ILE* 3.4 37.0 - - + +
106D GLN 3.8 0.9 - - - +
107D ASN* 1.3 78.8 - - - +
109D ILE* 1.3 65.6 + - + +
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Residues in contact with ILE 109 (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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35D TYR* 4.2 13.5 - - + -
36D HIS* 3.7 26.9 - - + +
37D ALA* 4.8 0.4 - - - +
38D ASN* 4.3 3.8 - - - +
86D LEU* 3.3 4.8 - - - -
87D ARG* 3.0 56.3 + - + +
88D PRO 4.8 4.3 - - - +
89D MET* 4.4 16.2 - - + -
107D ASN 3.6 0.6 - - - -
108D MET* 1.3 89.1 - - + +
110D VAL* 1.3 72.6 + - - +
111D GLU* 3.2 8.3 + - + +
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Residues in contact with VAL 110 (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* 3.5 31.0 - - + +
13D LYS* 3.9 5.8 - - + +
38D ASN* 2.8 50.1 + - + +
39D TYR* 4.7 3.4 - - - +
40D CYS* 4.0 2.9 - - - -
83D PRO* 3.8 26.0 - - + -
85D LYS 3.9 3.6 - - - +
86D LEU* 4.3 6.7 - - + -
108D MET 4.1 0.8 + - - -
109D ILE* 1.3 70.1 - - - +
111D GLU* 1.3 60.2 - - - +
112D GLU 3.6 24.0 - - - +
113D CYS* 3.7 22.2 - - - -
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Residues in contact with GLU 111 (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* 3.7 14.8 + - - -
13D LYS* 3.1 29.9 + - - +
85D LYS* 2.5 55.9 + - - +
86D LEU* 3.8 2.7 - - - -
87D ARG* 2.5 40.4 - - - +
109D ILE* 3.7 12.4 - - + +
110D VAL* 1.3 73.4 - - - +
112D GLU* 1.3 70.7 + - + +
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Residues in contact with GLU 112 (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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13D LYS* 4.9 4.5 - - - +
83D PRO* 3.4 6.4 - - - +
84D THR* 2.8 37.6 + - - +
85D LYS* 3.2 35.5 + - + +
110D VAL* 3.6 4.0 - - - +
111D GLU* 1.3 93.4 - - + +
113D CYS* 1.3 60.9 - - - +
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Residues in contact with CYS 113 (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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11D CYS* 4.1 10.6 - - - +
12D CYS* 3.8 19.8 - - - -
13D LYS* 3.9 16.5 - - - +
39D TYR 4.2 0.2 - - - -
40D CYS* 2.0 57.9 - - + -
82D VAL 3.5 5.4 - - - -
84D THR* 3.4 8.2 + - - -
110D VAL* 3.7 10.1 - - - -
112D GLU* 1.3 76.7 - - - +
114D GLY* 1.3 57.9 + - - +
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Residues in contact with GLY 114 (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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11D CYS* 3.6 13.5 - - - -
80D CYS 3.5 0.3 - - - +
81D CYS* 3.6 0.3 - - - -
82D VAL* 3.0 34.1 + - - +
84D THR* 3.6 14.6 - - - +
113D CYS* 1.3 76.2 - - - +
115D CYS* 1.3 62.5 + - - -
116D SER 3.8 0.5 + - - -
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Residues in contact with CYS 115 (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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11D CYS* 3.8 8.1 - - - -
43D GLU 4.1 0.9 - - - -
44D CYS* 2.1 57.7 - - + -
45D PRO* 4.4 2.5 - - + -
46D SER* 3.3 36.2 + - - +
80D CYS 3.5 0.2 - - - -
82D VAL* 5.3 0.2 - - - -
84D THR* 5.5 2.9 - - - +
114D GLY* 1.3 71.4 - - - -
116D SER* 1.3 66.8 + - - +
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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