Contacts of the strand formed by residues 125 - 137 (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 ASN 125 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68C TRP 3.4 6.9 - - - +
69C ASN* 2.9 28.0 + - - +
120C ILE* 3.4 4.9 - - - +
121C PHE* 3.0 43.2 + - + +
123C ASN* 3.0 31.6 + - - +
124C GLY* 1.3 81.2 - - - +
126C VAL* 1.3 62.2 + - - +
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Residues in contact with VAL 126 (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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66C GLN 4.4 0.2 - - - -
67C LYS* 3.2 9.7 - - - +
68C TRP* 2.7 74.9 + - + +
70C ASP* 4.5 1.3 - - + -
73C LEU* 3.8 26.0 - - + -
93C ILE* 4.5 2.5 - - + -
118C LEU* 3.7 27.4 - - + -
119C ARG 3.5 3.1 - - - -
120C ILE* 4.3 3.4 - - + -
121C PHE* 4.7 2.7 - - - -
124C GLY 3.8 9.2 - - - +
125C ASN* 1.3 81.9 - - - +
127C LEU* 1.3 66.9 + - - +
128C TYR* 4.2 0.7 - - + +
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Residues in contact with LEU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204B THR* 4.2 14.1 - - + -
65C ARG* 4.2 23.3 - - + -
66C GLN 3.6 3.8 - - - +
67C LYS* 4.0 31.9 - - + -
117C LEU* 3.8 19.3 - - + +
118C LEU* 3.6 5.7 - - - +
119C ARG* 2.8 73.9 + - + +
121C PHE* 4.2 13.4 - - + -
126C VAL* 1.3 74.3 - - - +
128C TYR* 1.3 66.8 + - - +
129C SER* 5.1 0.4 - - - -
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Residues in contact with TYR 128 (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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64C LEU 3.5 1.4 - - - +
65C ARG* 3.4 1.8 - - - -
66C GLN* 2.9 60.4 + - - +
68C TRP* 3.8 33.0 - + + -
90C LEU* 3.5 38.6 - - + +
95C LYS* 4.0 30.6 - - + +
96C PRO* 5.6 1.8 - - + -
116C LYS* 4.4 7.3 - - + -
117C LEU 3.4 7.4 - - - -
118C LEU* 5.1 0.2 - - + -
126C VAL* 4.5 3.4 - - + -
127C LEU* 1.3 76.7 - - - +
129C SER* 1.3 70.8 + - - +
130C ILE* 3.7 31.9 - - + +
112D THR* 4.9 12.5 + - - -
113D THR* 6.1 0.6 - - + +
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Residues in contact with SER 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B PHE* 3.6 7.6 - - - -
204B THR* 5.0 2.7 - - - -
63C PHE* 4.0 9.0 - - - +
64C LEU 3.2 3.9 + - - -
65C ARG* 3.2 35.2 + - - -
116C LYS* 3.3 3.3 - - - +
117C LEU* 2.8 61.1 + - - +
127C LEU* 4.2 1.5 - - - -
128C TYR* 1.3 77.6 - - - +
130C ILE* 1.3 63.0 + - - +
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Residues in contact with ILE 130 (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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159B PHE* 4.1 4.3 - - - -
62C ILE 3.7 0.5 - - - +
63C PHE* 3.5 1.1 - - - -
64C LEU* 2.8 61.8 + - + +
66C GLN* 5.2 0.7 - - - +
108C PHE* 3.4 35.9 - - + -
115C ASN 3.6 10.5 - - - +
116C LYS* 3.5 26.0 - - + -
128C TYR* 3.7 27.1 - - + +
129C SER* 1.3 76.9 + - - +
131C ARG* 1.3 73.0 + - - +
132C LEU* 3.8 10.2 + - + +
112D THR* 4.9 5.2 - - + -
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Residues in contact with ARG 131 (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* 3.5 18.8 - - - +
100B PHE 3.5 12.9 + - - -
101B ALA 3.5 12.1 + - - -
103B GLU* 2.9 48.4 + - - -
159B PHE* 3.7 9.3 - - + -
46C ASN* 4.0 0.6 - - - +
61C ASN* 3.1 25.4 + - - +
62C ILE 3.3 10.8 - - - +
63C PHE* 3.7 20.0 - - + -
108C PHE* 4.1 0.3 - - - -
109C HIS* 3.4 34.0 + - + -
115C ASN* 3.0 48.5 + - + +
130C ILE* 1.3 76.8 - - - +
132C LEU* 1.3 71.7 + - - +
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Residues in contact with LEU 132 (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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60C VAL 3.8 0.5 - - - +
61C ASN* 3.3 7.0 + - - -
62C ILE* 2.9 42.4 + - + +
64C LEU* 4.2 14.8 - - + -
100C PHE* 3.7 34.3 - - + -
107C ASN 3.6 9.2 - - - +
108C PHE* 3.6 29.4 - - + -
109C HIS* 4.0 1.3 - - - -
130C ILE* 4.1 11.9 - - + +
131C ARG* 1.3 83.8 - - - +
133C THR* 1.3 62.0 + - - +
134C LEU* 4.1 9.4 + - + -
111D VAL* 3.8 20.2 - - + -
112D THR* 4.1 9.9 - - + -
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Residues in contact with THR 133 (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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104B LYS* 4.8 5.3 + - - +
59C ARG* 3.9 34.5 - - + +
60C VAL 3.3 9.6 - - - +
61C ASN* 2.9 12.7 + - + +
105C GLY 4.5 0.2 - - - -
106C ALA* 3.2 5.5 - - - -
107C ASN* 3.0 49.7 + - - +
109C HIS* 2.7 29.4 + - - -
132C LEU* 1.3 73.0 - - - +
134C LEU* 1.3 65.3 + - - +
135C THR* 5.6 0.4 - - - +
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Residues in contact with LEU 134 (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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58C TYR 3.7 0.9 - - - +
59C ARG* 3.2 6.9 - - - +
60C VAL* 2.9 49.2 + - + +
62C ILE* 4.0 15.5 - - + -
100C PHE* 3.6 56.1 - - + -
103C GLU* 4.5 3.1 - - + -
105C GLY 3.4 2.7 - - - +
106C ALA* 3.5 26.7 - - + -
132C LEU* 4.4 14.4 - - + -
133C THR* 1.3 79.8 - - - +
135C THR* 1.3 61.4 + - - +
136C LEU* 3.8 18.1 + - + -
154C MET* 4.7 0.9 - - - -
111D VAL* 4.6 0.9 - - + -
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Residues in contact with THR 135 (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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57C ASP* 3.9 28.0 - - + +
58C TYR 3.3 11.4 - - - +
59C ARG* 3.9 17.7 - - + +
103C GLU* 3.5 3.3 - - - -
104C LYS* 2.7 40.5 + - + -
105C GLY* 2.7 24.1 + - - +
133C THR* 5.6 0.3 - - - +
134C LEU* 1.3 71.5 - - - +
136C LEU* 1.3 55.6 + - - +
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Residues in contact with LEU 136 (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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57C ASP* 3.1 4.6 - - - +
58C TYR* 2.8 69.8 + - + +
60C VAL* 4.0 15.0 - - + -
100C PHE* 4.2 9.4 - - + -
102C ASN* 3.4 22.9 - - - +
103C GLU* 3.7 27.6 - - + +
104C LYS* 4.5 1.1 - - - -
134C LEU* 4.0 15.7 - - + +
135C THR* 1.3 75.0 - - - +
137C SER* 1.3 63.1 - - - +
154C MET* 3.8 31.2 - - + -
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Residues in contact with SER 137 (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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56C MET 3.8 8.5 - - - -
58C TYR* 4.3 2.8 - - - -
102C ASN* 2.9 43.8 + - - +
104C LYS* 3.9 22.1 - - - +
136C LEU* 1.3 73.6 - - - +
138C CYS* 1.3 59.6 + - - +
139C PRO* 3.8 12.9 - - - +
153C ILE* 4.4 4.3 + - - +
47D SER* 6.5 1.1 - - - -
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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