Contacts of the strand formed by residues 110 - 126 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLN 3.7 0.7 - - - +
98B ARG* 3.4 6.3 - - - +
99B LEU* 3.0 32.4 + - + +
104B SER* 4.8 9.0 - - - -
106B THR* 4.3 13.9 - - + +
108B SER 3.4 7.6 + - - +
109B PRO* 1.3 76.7 - - - +
111B ILE* 1.3 67.6 + - - +
112B SER* 4.0 3.3 + - - -
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Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ARG* 3.6 36.8 - - - +
97B GLN 3.4 11.9 - - - +
98B ARG* 4.5 10.3 - - + -
110B ALA* 1.3 79.3 - - - +
112B SER* 1.3 66.0 + - - +
113B SER* 4.2 1.4 + - - -
324C TRP* 3.5 33.2 - - + -
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Residues in contact with SER 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B THR 3.6 0.9 - - - +
96B ARG* 3.6 1.9 - - - -
97B GLN* 3.1 57.0 + - - +
99B LEU* 4.2 8.3 - - - +
110B ALA* 4.0 4.3 - - - -
111B ILE* 1.3 75.0 - - - +
113B SER* 1.3 60.6 + - - +
311B ARG* 4.1 15.9 - - - +
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Residues in contact with SER 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B THR 3.0 10.3 - - - -
96B ARG* 3.8 27.8 + - - -
111B ILE* 4.2 1.5 + - - -
112B SER* 1.3 75.5 - - - +
114B GLN* 1.3 62.1 + - - +
115B TYR* 4.2 8.6 - - - -
311B ARG* 2.7 57.9 + - - +
312B GLN* 5.4 0.2 - - - +
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Residues in contact with GLN 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 5.9 3.7 - - - +
103A LEU* 3.6 31.3 - - + +
93B SER* 5.8 0.2 - - - -
94B GLY* 3.5 2.3 + - - -
95B THR* 3.0 48.1 + - + +
113B SER* 1.3 76.4 - - - +
115B TYR* 1.3 67.2 + - - +
309B MET* 4.3 16.4 - - - +
310B SER 3.4 6.1 - - - +
311B ARG* 5.0 5.0 - - - +
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Residues in contact with TYR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B SER* 3.5 6.3 - - - +
94B GLY* 3.7 19.7 - - - -
95B THR 4.6 2.2 - - - -
96B ARG* 3.2 34.8 + - + -
113B SER* 4.2 9.6 - - - -
114B GLN* 1.3 80.9 - - - +
116B GLY* 1.3 59.3 + - - +
309B MET* 3.2 8.1 - - - +
310B SER 2.7 36.4 + - - +
311B ARG 3.7 15.7 - - - -
312B GLN* 3.7 5.4 - - - +
313B LEU* 3.4 58.0 - - + +
316B LEU* 3.4 16.9 - - + +
328C PRO* 5.9 3.6 - - + -
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Residues in contact with GLY 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ASP 3.5 1.7 - - - +
92B GLY* 3.3 3.1 - - - -
93B SER* 2.7 45.5 + - - +
115B TYR* 1.3 74.8 - - - +
117B VAL* 1.3 65.9 + - - +
118B THR* 5.5 1.8 - - - -
308B THR 3.4 9.9 - - - -
309B MET* 3.9 11.0 - - - -
316B LEU* 3.9 1.5 - - - +
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B VAL* 4.3 19.7 - - + -
91B ASP 3.4 4.3 - - - +
92B GLY* 4.5 8.1 - - - -
116B GLY* 1.3 78.8 - - - +
118B THR* 1.3 64.0 + - - +
307B GLY* 3.6 1.9 - - - -
308B THR* 3.0 35.7 + - - +
316B LEU* 4.0 23.5 - - + +
317B PHE* 3.6 33.3 - - + -
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Residues in contact with THR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLY 3.8 0.2 - - - +
90B VAL* 3.3 9.1 - - - +
91B ASP* 2.9 56.2 + - + +
116B GLY* 5.6 1.1 - - - -
117B VAL* 1.3 77.8 - - - +
119B LEU* 1.3 67.6 + - - +
120B GLY 4.3 0.4 - - - +
305B ASN* 2.9 42.1 + - + +
306B ALA 2.9 16.8 + - - -
307B GLY* 4.2 1.6 - - - -
308B THR 5.2 0.9 - - - -
309B MET* 6.5 0.4 - - - -
323B SER* 5.9 1.3 - - - -
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ILE* 4.1 16.4 - - + -
89B GLY 3.4 14.8 - - - +
90B VAL* 3.8 19.7 - - + -
118B THR* 1.3 77.9 + - - +
120B GLY* 1.3 58.4 + - - +
305B ASN* 3.5 4.3 - - - -
306B ALA* 2.9 30.5 + - - +
334C ILE* 4.0 16.8 - - + -
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Residues in contact with GLY 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ARG 3.5 1.9 - - - +
88B ILE* 4.2 13.7 - - - -
89B GLY 3.0 32.5 + - - +
91B ASP* 4.8 6.8 + - - +
118B THR* 5.5 0.4 - - - +
119B LEU* 1.3 76.5 - - - +
121B THR* 1.3 61.0 + - - -
122B THR* 5.2 0.3 + - - -
304B ALA 3.4 10.3 - - - -
305B ASN* 4.1 4.4 - - - +
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Residues in contact with THR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PRO* 4.3 14.4 - - + -
87B ARG* 3.2 26.1 + - - +
88B ILE* 4.9 2.9 - - - +
120B GLY* 1.3 73.8 - - - -
122B THR* 1.3 73.6 + - - +
124B TRP* 3.6 28.3 - - + +
302B LEU* 4.0 13.2 - - + +
303B THR* 3.6 5.9 - - - +
304B ALA* 2.9 47.5 + - + +
305B ASN* 5.0 2.9 + - - +
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Residues in contact with THR 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ARG* 4.3 4.7 + - - +
91B ASP* 4.1 16.5 + - - -
121B THR* 1.3 81.7 + - - +
123B ALA* 1.3 77.1 + - + +
124B TRP* 3.4 1.8 + - - -
303B THR* 4.1 14.4 - - + +
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Residues in contact with ALA 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B THR* 1.3 80.1 - - + +
124B TRP* 1.3 62.8 + - - +
125B GLU* 3.5 4.7 + - - +
301B SER* 3.8 16.6 - - - +
302B LEU 3.3 6.2 + - - -
303B THR* 3.2 16.1 + - - +
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Residues in contact with TRP 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ASP 5.0 3.4 - - - -
84B LEU 3.6 18.5 + - - -
85B PHE 4.0 4.5 - - - -
86B PRO* 3.5 52.0 - - + -
87B ARG 5.3 0.2 - - - +
121B THR* 3.6 22.2 - - + +
122B THR 3.4 1.4 - - - -
123B ALA* 1.3 71.2 - - - +
125B GLU* 1.3 76.7 + - - +
126B LEU* 3.4 36.4 + - + +
301B SER* 3.3 4.3 - - - -
302B LEU* 2.9 64.5 + - + +
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B ASP 5.0 0.4 + - - +
84B LEU 5.1 1.7 - - - +
123B ALA 3.5 5.6 + - - +
124B TRP* 1.3 84.7 + - - +
126B LEU* 1.3 69.7 - - - +
127B ASP* 3.2 6.3 + - - +
131B ARG* 3.1 47.4 + - - +
132B LEU* 3.8 32.6 - - + +
299B SER* 4.5 16.6 + - - +
300B ILE 3.4 13.9 - - - +
301B SER* 4.6 2.9 - - - +
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B TRP* 3.4 40.2 + - + -
125B GLU* 1.3 72.9 - - - +
127B ASP* 1.3 61.3 + - - +
128B LEU* 2.8 18.7 + - + +
300B ILE* 2.9 50.9 + - + +
301B SER 5.0 0.2 - - - +
302B LEU* 4.4 26.5 - - + -
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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