Contacts of the strand formed by residues 89 - 105 (chain W) in PDB entry 3S1K
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 GLN 89 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B ALA 3.5 18.8 + - - -
18B LEU* 3.4 35.0 + - - +
19B LEU 3.9 7.9 + - - -
20B PRO* 4.7 12.9 - - + +
27B PHE* 5.8 0.2 - - - -
81W MET* 4.2 9.1 - - + +
82W ARG 3.1 14.6 - - - +
83W ILE* 3.7 31.8 - - + +
88W GLY* 1.3 77.4 - - - -
90W HIS* 1.3 66.7 + - - +
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Residues in contact with HIS 90 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 3.6 11.7 - - - -
80W ILE 5.5 0.2 - - - -
81W MET* 3.4 2.6 - - - +
82W ARG* 2.8 89.5 + - + -
88W GLY 6.0 0.9 - - - -
89W GLN* 1.3 77.8 - - - +
91W ILE* 1.3 61.4 + - - +
92W GLY* 3.9 14.8 + - - -
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Residues in contact with ILE 91 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE* 3.7 44.8 - - + +
17B ALA* 3.8 15.7 - - + -
18B LEU* 3.5 9.6 - - + +
17V PHE* 4.0 15.0 - - + -
79W GLN* 4.1 25.1 - - + -
80W ILE 3.4 9.9 - - - +
81W MET* 3.5 39.3 - - + -
90W HIS* 1.3 74.1 - - - +
92W GLY* 1.3 60.6 + - - +
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Residues in contact with GLY 92 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79W GLN* 3.2 6.9 - - - -
80W ILE* 2.8 34.0 + - - +
90W HIS* 3.9 14.3 + - - -
91W ILE* 1.3 75.0 - - - +
93W GLU* 1.3 65.8 + - - -
94W MET* 5.3 1.6 - - - -
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Residues in contact with GLU 93 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14V VAL* 3.9 25.9 - - + +
77W THR* 3.6 25.0 - - + +
78W MET 3.2 5.8 - - - +
79W GLN* 4.8 9.6 + - + +
92W GLY* 1.3 77.2 - - - +
94W MET* 1.3 65.1 + - - +
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Residues in contact with MET 94 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35W ILE* 3.9 13.0 - - + -
39W TYR* 3.6 42.2 - - + +
42W GLU* 5.9 0.7 - - + -
47W PHE* 3.4 40.2 - - + -
76W ILE 3.7 0.3 - - - +
77W THR* 3.3 4.0 - - - -
78W MET 2.8 34.3 + - - -
80W ILE* 3.7 26.0 - - + +
82W ARG* 6.0 0.9 - - - -
92W GLY 4.0 2.0 + - - +
93W GLU* 1.3 77.6 - - - +
95W SER* 1.3 63.5 + - - +
96W PHE* 3.8 18.3 - - + -
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Residues in contact with SER 95 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39W TYR* 2.7 36.0 + - - -
75W ASN* 4.1 19.9 + - - +
76W ILE 3.3 5.4 + - - -
77W THR* 3.4 18.0 + - - +
94W MET* 1.3 72.3 - - - +
96W PHE* 1.3 66.7 + - - +
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Residues in contact with PHE 96 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35W ILE* 4.1 24.2 - - + -
38W GLU* 4.2 23.8 - - + -
39W TYR* 3.9 18.2 - + - -
52W VAL* 4.0 41.1 - - + -
54W LEU* 3.5 22.0 - - + -
75W ASN* 3.5 4.2 - - - -
76W ILE* 2.7 43.9 + - + +
78W MET* 4.2 16.6 - - + -
80W ILE* 4.4 6.5 - - + -
94W MET* 3.8 35.2 - - + -
95W SER* 1.3 78.5 - - - +
97W LEU* 1.3 63.5 + - - +
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Residues in contact with LEU 97 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38W GLU* 4.7 7.1 + - - +
54W LEU* 3.9 3.1 - - - +
56W ARG* 2.4 46.3 + - - +
73W GLU* 3.4 39.0 - - + +
74W SER 3.6 6.1 - - - +
75W ASN* 4.1 15.9 - - - +
96W PHE* 1.3 72.3 - - - +
98W GLN* 1.3 78.0 + - - +
99W HIS* 4.2 14.1 - - + +
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Residues in contact with GLN 98 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53W PRO 4.2 3.6 - - - +
54W LEU* 3.8 10.1 - - + +
55W MET* 3.1 44.9 + - + +
56W ARG* 4.3 0.7 - - - +
73W GLU* 3.2 10.7 - - - +
74W SER* 2.6 51.7 + - - +
76W ILE* 3.7 42.9 - - + +
78W MET* 5.4 0.3 - - - +
97W LEU* 1.3 78.8 - - - +
99W HIS* 1.3 66.2 + - - +
100W ASN* 4.8 5.6 - - - +
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Residues in contact with HIS 99 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28W PRO* 3.7 9.1 - - - +
55W MET* 2.8 33.0 + - - +
56W ARG* 3.4 25.7 + - + -
57W CYS* 2.9 45.2 + - + +
70W PRO* 3.7 36.4 - - + +
72W GLU 3.7 3.1 - - - -
73W GLU* 3.9 13.1 + - + -
97W LEU* 4.2 10.8 - - + +
98W GLN* 1.3 79.2 - - - +
100W ASN* 1.3 64.5 + - - +
101W LYS 4.9 0.2 - - - +
102W CYS* 4.3 2.2 - - - -
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Residues in contact with ASN 100 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28W PRO* 3.5 14.2 - - - +
55W MET* 6.0 0.4 - - - +
72W GLU* 2.7 36.3 + - - +
73W GLU 3.1 13.3 + - - +
74W SER* 3.0 38.3 + - - -
98W GLN* 4.8 6.9 - - - +
99W HIS* 1.3 78.6 + - - +
101W LYS* 1.3 65.4 + - + +
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Residues in contact with LYS 101 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28W PRO* 4.3 2.0 - - - -
70W PRO* 3.4 6.2 - - - +
71W THR* 2.8 44.8 + - - +
72W GLU* 3.0 38.7 + - + +
100W ASN* 1.3 84.3 + - - +
102W CYS* 1.3 60.1 + - - +
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Residues in contact with CYS 102 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26W CYS* 4.0 8.0 - - - +
27W HIS* 4.0 11.0 - - - -
28W PRO* 3.6 25.6 - - - +
57W CYS* 2.0 54.5 - - - -
68W CYS* 3.9 13.7 - - - -
69W VAL 3.4 4.7 - - - +
71W THR* 4.3 1.6 + - - -
99W HIS* 4.3 2.7 - - - -
101W LYS* 1.3 78.8 - - - +
103W GLU* 1.3 69.1 + - - +
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Residues in contact with GLU 103 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25W TYR* 6.5 0.2 - - - -
26W CYS* 4.1 7.4 - - - -
67W GLU 3.1 2.8 - - - +
68W CYS* 3.4 0.2 - - - -
69W VAL* 2.8 34.5 + - - +
71W THR* 3.3 30.3 + - + +
102W CYS* 1.3 79.9 - - - +
104W CYS* 1.3 63.2 + - - +
105W ARG* 3.0 35.3 + - - -
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Residues in contact with CYS 104 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25W TYR* 3.2 32.7 + - - +
26W CYS* 3.9 8.0 - - - +
61W CYS* 2.0 61.2 - - + -
66W LEU* 3.8 21.4 - - + +
67W GLU 3.4 0.2 - - - -
103W GLU* 1.3 73.4 - - - +
105W ARG* 1.3 66.6 + - - +
106W PRO* 4.6 0.7 - - - +
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Residues in contact with ARG 105 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66W LEU* 3.2 6.3 - - - -
67W GLU* 2.7 40.1 + - + +
69W VAL* 3.7 22.7 - - + +
70W PRO 5.5 1.0 + - - -
71W THR* 3.6 17.5 - - - +
103W GLU* 3.0 47.8 + - - -
104W CYS* 1.3 82.1 - - - +
106W PRO* 1.3 77.3 - - + +
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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