Contacts of the strand formed by residues 110 - 126 (chain C) in PDB entry 3D5K
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 ALA 110 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97C GLN 3.7 1.7 - - - +
98C ARG* 3.5 5.3 - - - +
99C LEU* 3.0 33.7 + - - +
104C SER* 4.4 12.5 - - - -
106C THR* 4.5 9.2 - - + +
108C SER 3.4 7.8 + - - +
109C PRO* 1.3 74.6 - - - +
111C ILE* 1.3 66.5 + - - +
112C SER* 4.0 1.3 + - - -
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Residues in contact with ILE 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A TRP* 4.0 16.4 - - + +
96C ARG* 3.8 49.1 - - + +
97C GLN 3.4 9.2 - - - +
98C ARG* 3.3 42.8 - - + +
110C ALA* 1.3 76.5 - - - +
112C SER* 1.3 62.8 + - - +
113C SER* 4.0 4.5 + - - +
311C ARG* 5.0 1.4 + - - -
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Residues in contact with SER 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C THR* 4.1 2.9 - - - +
96C ARG* 3.7 1.4 + - - -
97C GLN* 3.1 50.7 + - - +
99C LEU* 4.1 10.1 - - - +
110C ALA 4.0 1.9 + - - -
111C ILE* 1.3 72.3 - - - +
113C SER* 1.3 60.0 + - - +
114C GLN* 5.6 3.4 - - - +
311C ARG* 3.7 16.8 - - - +
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Residues in contact with SER 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C THR 3.1 11.4 - - - -
96C ARG* 3.6 24.5 - - - -
111C ILE* 4.0 5.9 + - - +
112C SER* 1.3 73.9 - - - +
114C GLN* 1.3 60.5 + - - +
115C TYR* 4.6 9.6 + - - -
311C ARG* 2.9 49.9 + - - +
312C GLN* 5.6 1.2 - - - +
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Residues in contact with GLN 114 (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 LEU* 5.9 0.5 - - - +
103B LEU* 3.8 26.9 - - + +
93C SER* 4.8 0.3 + - - -
94C GLY* 3.6 0.9 - - - -
95C THR* 2.8 59.0 + - + +
97C GLN* 6.1 1.2 - - - +
112C SER* 5.6 3.7 - - - +
113C SER* 1.3 76.1 - - - +
115C TYR* 1.3 66.0 + - - +
309C MET* 3.4 24.9 - - - +
310C SER 3.4 4.9 - - - +
311C ARG* 4.1 10.3 - - - +
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Residues in contact with TYR 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A PRO* 6.3 1.3 - - + -
93C SER* 3.3 10.8 - - - +
94C GLY* 4.0 20.0 - - - -
95C THR 5.0 3.8 - - - -
96C ARG* 5.0 10.0 - - + +
113C SER* 4.6 13.3 - - - -
114C GLN* 1.3 75.8 - - - +
116C GLY* 1.3 60.1 + - - +
309C MET* 3.5 14.0 - - - +
310C SER 2.7 27.8 + - - +
311C ARG 3.4 22.9 - - - -
312C GLN* 3.5 3.6 - - - -
313C LEU* 3.4 53.7 - - + +
316C LEU* 4.0 19.7 - - + -
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Residues in contact with GLY 116 (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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91C ASP 3.5 1.2 - - - +
92C GLY* 3.4 2.9 - - - -
93C SER* 2.7 43.2 + - - +
115C TYR* 1.3 77.5 - - - +
117C VAL* 1.3 67.1 + - - +
118C THR* 4.0 2.2 - - - -
308C THR 3.3 11.9 - - - -
309C MET* 4.1 9.2 - - - -
316C LEU* 3.8 2.6 - - - +
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Residues in contact with VAL 117 (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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90C VAL* 4.2 20.2 - - + -
91C ASP 3.5 4.3 - - - +
92C GLY* 4.9 5.4 - - - -
116C GLY* 1.3 76.7 - - - +
118C THR* 1.3 62.1 + - - +
307C GLY* 3.6 2.8 - - - -
308C THR* 2.9 41.3 + - + +
316C LEU* 4.1 20.8 - - + +
317C PHE* 4.2 24.9 - - + -
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Residues in contact with THR 118 (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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89C GLY 3.9 0.2 - - - +
90C VAL* 3.4 6.5 - - - +
91C ASP* 2.7 63.4 + - + +
116C GLY 5.4 1.6 - - - -
117C VAL* 1.3 75.9 - - - +
119C LEU* 1.3 62.8 + - - +
305C ASN* 3.4 39.8 + - + +
306C ALA 3.4 14.7 + - - -
307C GLY* 3.7 2.6 + - - -
308C THR 5.2 0.9 - - - -
309C MET* 5.8 4.2 - - - +
323C SER* 4.7 5.1 + - - -
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Residues in contact with LEU 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ILE* 4.4 9.9 - - + -
88C ILE* 4.3 16.8 - - + -
89C GLY 3.6 17.9 - - - +
90C VAL* 3.8 22.2 - - + -
118C THR* 1.3 75.1 - - - +
120C GLY* 1.3 58.9 + - - +
305C ASN* 3.3 3.0 - - - -
306C ALA* 2.8 43.7 + - + +
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Residues in contact with GLY 120 (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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87C ARG 3.6 0.3 - - - +
88C ILE* 3.3 13.9 - - - -
89C GLY 3.0 33.5 + - - +
91C ASP* 4.6 7.7 + - - +
118C THR 4.3 0.2 - - - -
119C LEU* 1.3 76.1 - - - +
121C THR* 1.3 60.3 + - - -
304C ALA 3.2 11.4 - - - -
305C ASN* 3.9 4.4 - - - +
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Residues in contact with THR 121 (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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86C PRO* 3.9 13.6 - - + +
87C ARG* 2.8 34.1 + - - +
88C ILE* 4.6 3.4 - - - -
91C ASP* 5.8 0.4 - - - -
120C GLY* 1.3 72.4 - - - -
122C THR* 1.3 72.3 + - - +
124C TRP* 3.9 19.6 - - + +
302C LEU* 3.9 19.3 - - + +
303C THR* 3.4 15.4 - - - +
304C ALA* 2.7 32.8 + - + +
305C ASN* 4.9 1.6 + - - +
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Residues in contact with THR 122 (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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87C ARG* 4.3 6.5 + - - +
91C ASP* 4.7 11.8 + - - -
121C THR* 1.3 83.4 + - - +
123C ALA* 1.3 76.8 + - + +
124C TRP* 3.3 3.4 + - - -
303C THR* 4.2 14.6 - - + +
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Residues in contact with ALA 123 (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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122C THR* 1.3 80.7 - - + +
124C TRP* 1.3 62.9 + - - +
125C GLU* 3.1 7.3 + - - +
301C SER* 4.0 16.2 + - - +
302C LEU 3.8 1.5 + - - -
303C THR* 3.4 14.7 + - - -
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Residues in contact with TRP 124 (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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83C ASP 4.7 5.6 - - - -
84C LEU 3.2 24.4 + - - -
85C PHE* 3.5 9.6 - + - -
86C PRO* 3.5 46.4 - - + -
87C ARG 5.2 0.9 - - - +
121C THR* 3.9 20.4 - - + +
122C THR 3.3 2.5 - - - -
123C ALA* 1.3 73.0 - - - +
125C GLU* 1.3 73.0 + - - +
126C LEU* 3.5 32.5 + - + +
301C SER* 3.4 1.7 - - - -
302C LEU* 2.9 64.7 + - + +
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Residues in contact with GLU 125 (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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83C ASP 4.9 0.9 + - - +
84C LEU* 4.9 2.3 - - - +
123C ALA 3.1 8.4 + - - +
124C TRP* 1.3 85.7 + - - +
126C LEU* 1.3 69.4 + - - +
127C ASP* 3.8 3.8 + - - +
131C ARG* 3.1 47.5 + - - +
132C LEU* 3.8 32.6 - - + +
299C SER* 4.5 16.9 + - - +
300C ILE 3.5 13.2 - - - +
301C SER* 4.4 3.8 - - - +
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Residues in contact with LEU 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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124C TRP* 3.5 49.3 + - + +
125C GLU* 1.3 79.2 - - - +
127C ASP* 1.3 59.9 + - - +
128C LEU* 3.2 9.3 + - + +
300C ILE* 2.9 52.7 + - + +
302C LEU* 4.7 18.4 - - + -
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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