Contacts of the strand formed by residues 57 - 69 (chain C) in PDB entry 5TIN
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 ASP 57 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50C SER 3.5 2.8 - - - +
51C ILE* 3.6 2.6 - - - +
52C ALA* 2.9 34.8 + - - +
55C THR* 2.7 27.8 + - - -
56C MET* 1.3 75.3 - - - +
58C TYR* 1.3 65.3 + - - +
104C LYS* 2.9 37.1 + - + +
135C THR* 3.9 15.8 - - + +
136C LEU 3.1 15.9 - - - +
138C CYS* 3.9 6.3 - - - +
140C MET* 4.5 1.7 - - - +
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Residues in contact with TYR 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C PHE* 3.7 34.5 - + - -
50C SER 3.6 9.0 - - - -
51C ILE* 3.9 24.7 - - + -
57C ASP* 1.3 75.1 - - - +
59C ARG* 1.3 62.6 + - - +
60C VAL* 3.8 20.4 - - + -
134C LEU 3.7 0.2 - - - +
135C THR* 3.3 6.6 - - - +
136C LEU* 2.8 70.0 + - + +
137C SER 4.3 0.4 - - - -
138C CYS* 3.8 18.2 - - + -
152C CYS* 3.6 23.8 - - + -
153C ILE 2.7 30.5 + - - -
154C MET* 4.0 0.3 + - - +
214C PHE* 4.0 11.9 - + - -
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Residues in contact with ARG 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B THR* 6.3 0.2 - - - -
57B ASP* 5.5 0.2 + - - -
104B LYS* 3.5 53.0 + - - +
47C SER* 4.6 1.5 + - - +
48C PHE* 3.5 0.2 - - - -
49C GLY 2.9 40.7 + - - +
50C SER* 3.7 26.3 + - - +
58C TYR* 1.3 75.8 - - - +
60C VAL* 1.3 73.5 + - - +
133C THR* 3.9 27.3 - - + +
134C LEU 3.2 8.7 - - - +
135C THR* 3.9 16.8 - - + +
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Residues in contact with VAL 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ILE* 4.9 2.7 - - + -
47C SER* 3.3 9.4 - - - +
48C PHE* 3.7 28.5 - - + -
58C TYR* 3.8 16.6 - - + -
59C ARG* 1.3 82.4 - - - +
61C ASN* 1.3 60.6 + - - +
62C ILE* 3.8 22.0 - - + -
132C LEU 3.8 0.2 - - - +
133C THR* 3.3 6.2 - - - +
134C LEU* 2.9 54.6 + - + +
136C LEU* 4.0 13.5 - - + -
154C MET* 4.0 12.1 - - + -
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Residues in contact with ASN 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B GLU 4.7 3.4 + - - -
104B LYS* 6.0 0.4 - - - +
46C ASN* 2.8 51.7 + - - +
47C SER* 3.0 30.8 + - - +
60C VAL* 1.3 73.4 - - - +
62C ILE* 1.3 64.7 + - - +
63C PHE* 4.7 0.2 - - - -
109C HIS* 3.3 19.4 + - - -
131C ARG* 3.1 24.2 + - - +
132C LEU 3.3 6.0 + - - -
133C THR* 2.9 26.5 + - + +
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Residues in contact with ILE 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ILE* 4.3 17.0 - - + -
44C PHE 3.2 12.6 - - - +
45C ILE* 4.3 15.0 - - + -
46C ASN 4.4 0.4 - - - +
60C VAL* 3.8 23.1 - - + -
61C ASN* 1.3 80.3 - - - +
63C PHE* 1.3 72.8 + - - +
64C LEU* 4.2 14.1 - - + +
100C PHE* 4.1 17.5 - - + -
130C ILE 3.7 0.2 - - - +
131C ARG* 3.3 5.1 - - - +
132C LEU* 2.9 47.3 + - + +
134C LEU* 4.0 22.4 - - + -
154C MET* 4.5 8.7 - - + -
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Residues in contact with PHE 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B PHE* 4.2 13.7 - + - -
101B ALA* 6.3 0.4 - - + -
157B GLU* 4.9 0.2 - - - -
159B PHE* 3.8 24.7 - + - -
202B TYR* 3.7 39.5 - + - -
43C ILE* 3.3 6.9 - - - +
44C PHE* 2.9 43.7 + + + -
46C ASN* 4.7 14.8 - - + -
61C ASN* 4.7 4.0 - - - -
62C ILE* 1.3 80.2 - - - +
64C LEU* 1.3 61.1 + - - +
65C ARG* 3.7 32.0 - - - +
129C SER* 4.0 7.2 - - - +
130C ILE 3.5 4.0 - - - +
131C ARG* 3.7 29.8 - - + -
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Residues in contact with LEU 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C CYS* 5.0 1.6 - - + -
42C ASN 4.0 2.0 - - - +
43C ILE* 4.0 20.6 - - + -
62C ILE* 3.9 12.6 - - + -
63C PHE* 1.3 71.6 - - - +
65C ARG* 1.3 68.6 + - - +
66C GLN* 3.8 22.4 + - + +
98C LEU* 3.9 17.5 - - + -
100C PHE* 4.2 9.6 - - + -
128C TYR 3.5 1.9 - - - +
129C SER* 3.2 3.8 - - - -
130C ILE* 2.8 45.2 + - + +
132C LEU* 4.2 4.5 - - + -
156C LEU* 4.0 21.1 - - + -
112D THR* 3.8 28.9 - - + -
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Residues in contact with ARG 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B TYR* 3.8 23.8 - - - +
203B ASN* 3.4 17.4 + - - +
204B THR* 3.8 14.7 + - + +
40C THR 4.4 0.4 - - - -
41C CYS* 3.3 7.8 - - - +
42C ASN* 2.8 81.0 + - - +
44C PHE* 3.7 24.1 - - - +
63C PHE* 3.7 20.9 - - - +
64C LEU* 1.3 75.2 - - - +
66C GLN* 1.3 64.3 + - - +
67C LYS* 5.4 1.3 - - - -
127C LEU* 4.2 17.3 - - + -
128C TYR 3.4 3.1 - - - -
129C SER* 3.2 29.1 + - - +
177C GLN* 2.9 19.6 + - - -
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Residues in contact with GLN 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C VAL* 4.1 11.2 - - + +
40C THR 3.4 3.6 - - - -
41C CYS* 4.3 9.4 - - - -
64C LEU* 3.8 21.5 - - + +
65C ARG* 1.3 78.8 - - - +
67C LYS* 1.3 62.0 + - - +
68C TRP* 3.8 19.0 - - + -
96C PRO* 3.4 33.6 + - - +
98C LEU* 3.8 26.3 - - + +
126C VAL 3.8 0.5 - - - +
127C LEU* 3.6 3.8 - - - +
128C TYR* 2.9 60.2 + - + +
130C ILE* 5.2 1.4 - - - +
168C PHE* 4.8 0.2 - - - -
112D THR* 4.7 5.7 + - - +
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Residues in contact with LYS 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B ASN* 6.0 2.8 + - - -
38C GLN 3.7 0.7 - - - +
39C VAL* 3.3 2.4 - - - +
40C THR* 2.8 48.0 + - + +
42C ASN* 4.1 9.1 - - - +
65C ARG* 5.4 1.1 - - - -
66C GLN* 1.3 80.7 - - - +
68C TRP* 1.3 66.3 + - - +
126C VAL 3.2 10.3 - - - +
127C LEU* 4.0 26.5 - - + -
171C GLN* 2.7 32.1 + - - +
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Residues in contact with TRP 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C PRO* 4.3 2.7 - - + -
37C VAL* 4.0 10.3 - - + -
38C GLN 3.6 17.3 - - - +
39C VAL* 4.2 4.7 - - + -
66C GLN* 3.8 25.1 - - + -
67C LYS* 1.3 84.5 - - - +
69C ASN* 1.3 76.2 + - - +
70C ASP* 4.3 6.3 - - - +
90C LEU* 6.0 0.2 - - + -
93C ILE* 4.6 4.7 - - + -
94C TRP* 3.5 49.1 + + - -
95C LYS* 3.9 7.6 - - + -
96C PRO* 3.6 30.7 - - + -
125C ASN* 3.4 5.6 - - - +
126C VAL* 2.7 64.6 + - + +
128C TYR* 3.8 15.9 - + + -
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Residues in contact with ASN 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C PRO* 3.4 19.9 - - - +
31C ASN* 4.9 4.6 + - - +
37C VAL* 4.9 4.1 - - - +
38C GLN 4.7 1.6 + - - -
68C TRP* 1.3 79.2 - - - +
70C ASP* 1.3 58.0 - - - +
71C PRO* 3.3 24.9 - - - +
123C ASN* 3.0 29.6 + - - +
124C GLY 3.3 1.3 - - - -
125C ASN* 2.9 31.2 + - - +
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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