Contacts of the strand formed by residues 105 - 121 (chain B) in PDB entry 5AZS
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 GLU 105 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B GLN 3.8 0.7 - - - +
93B ARG* 3.5 2.2 - - - +
94B GLN* 2.8 42.2 + - + +
99B SER* 3.0 26.9 + - - +
100B ALA* 4.9 2.6 + - - +
101B GLY* 4.7 7.7 + - - +
103B ARG 3.0 5.4 + - - +
104B SER* 1.3 72.9 - - - +
106B VAL* 1.3 67.9 + - - +
107B ALA* 3.9 21.2 + - - +
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A TRP* 4.6 14.1 - - + +
91B ARG* 6.3 0.7 - - - +
92B GLN 3.5 4.0 - - - +
93B ARG* 3.8 42.6 - - + +
104B SER 4.1 3.0 + - - +
105B GLU* 1.3 77.4 - - - +
107B ALA* 1.3 59.5 + - - +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ASN* 4.1 1.6 - - - +
91B ARG* 3.5 2.3 - - - -
92B GLN* 3.0 37.1 + - + +
94B GLN* 5.8 6.3 - - + -
105B GLU* 3.9 21.2 - - - +
106B VAL* 1.3 73.0 - - - +
108B SER* 1.3 62.4 + - - +
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Residues in contact with SER 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ASN 3.3 5.2 - - - -
91B ARG* 3.9 18.7 + - - +
106B VAL 4.3 0.8 + - - -
107B ALA* 1.3 77.0 - - - +
109B SER* 1.3 64.2 + - - +
110B TYR* 3.7 24.3 + - - -
307B ALA* 2.7 42.3 + - - +
308B GLU* 4.2 9.2 + - - +
98C LEU* 4.4 2.8 - - - +
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Residues in contact with SER 109 (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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88B THR 3.8 2.3 - - - +
89B GLY* 3.7 1.7 - - - -
90B ASN* 2.6 41.4 + - - +
108B SER* 1.3 77.0 - - - +
110B TYR* 1.3 62.0 + - - +
111B GLN* 3.9 17.7 + - - +
306B SER 3.6 7.4 - - - -
98C LEU* 3.8 24.8 - - - +
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Residues in contact with TYR 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A PRO* 6.5 0.9 - - + -
88B THR 3.6 4.0 - - - +
89B GLY* 4.0 17.0 - - - -
90B ASN 5.2 0.4 - - - -
91B ARG* 3.1 43.5 + - + -
108B SER* 3.7 13.0 - - - -
109B SER* 1.3 72.8 - - - +
111B GLN* 1.3 59.7 + - - +
112B VAL* 6.0 0.7 - - + -
305B SER* 3.6 0.6 - - - -
306B SER 3.1 30.2 + - - +
307B ALA 3.5 21.3 - - - -
308B GLU* 3.9 3.8 - - + -
309B MET* 3.7 54.4 - - + +
312B LEU* 3.3 19.2 - - + +
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Residues in contact with GLN 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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87B ALA* 4.4 0.2 - - - -
88B THR* 2.7 73.6 + - + +
90B ASN* 5.9 2.8 - - - +
109B SER* 4.2 17.2 + - - +
110B TYR* 1.3 74.1 - - - +
112B VAL* 1.3 67.2 + - - +
301B SER* 5.4 5.2 + - - -
304B THR 3.6 5.4 - - - +
305B SER* 3.4 22.4 - - - +
312B LEU* 4.2 1.1 - - - -
319B SER* 5.0 4.5 + - - -
98C LEU* 6.1 1.8 - - - -
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Residues in contact with VAL 112 (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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86B ALA 3.6 11.2 - - - +
87B ALA* 3.8 17.7 - - + -
110B TYR* 6.0 0.9 - - + -
111B GLN* 1.3 82.1 - - - +
113B GLY* 1.3 63.6 + - - +
303B GLY* 3.7 1.3 - - - -
304B THR* 2.9 40.3 + - - +
312B LEU* 3.7 29.1 - - + +
313B PHE* 4.6 16.3 - - + -
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Residues in contact with GLY 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ALA* 4.7 0.4 - - - -
86B ALA* 2.7 43.9 + - - +
112B VAL* 1.3 79.6 - - - +
114B LEU* 1.3 68.3 + - - -
302B PHE 3.5 9.6 - - - -
303B GLY* 4.1 3.8 - - - -
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ILE* 6.0 1.6 - - + -
83B LEU* 3.6 34.3 - - + -
84B ASN 3.5 4.0 - - - +
85B ALA* 4.8 12.1 - - + -
113B GLY* 1.3 77.7 - - - -
115B ALA* 1.3 60.5 + - - +
301B SER* 3.6 2.1 - - - -
302B PHE* 2.7 53.3 + - + +
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Residues in contact with ALA 115 (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 LEU* 3.4 7.4 - - - +
84B ASN* 2.6 49.0 + - + +
86B ALA* 4.3 18.2 - - + -
114B LEU* 1.3 76.2 - - - +
116B LEU* 1.3 61.9 + - - +
117B PRO* 3.9 1.0 - - - +
300B GLY 3.4 9.9 - - - +
301B SER* 4.2 8.3 - - - +
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Residues in contact with LEU 116 (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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81B PRO* 4.4 13.0 - - + -
82B GLY 3.0 33.9 - - - +
83B LEU* 4.8 1.6 - - + +
115B ALA* 1.3 74.0 - - - +
117B PRO* 1.4 75.5 - - + +
119B TYR* 4.6 7.2 - - + -
298B LEU* 4.3 20.0 - - + +
299B THR* 3.6 12.5 - - - +
300B GLY* 2.7 42.0 + - - +
322B PHE* 6.3 2.9 - - + -
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Residues in contact with PRO 117 (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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335A ARG* 5.9 5.6 - - - +
82B GLY* 3.3 29.5 + - - +
83B LEU 4.2 0.9 - - - +
84B ASN* 4.4 23.6 - - + +
115B ALA 3.9 5.4 - - - +
116B LEU* 1.4 89.2 - - - +
118B GLU* 1.3 69.9 + - - +
119B TYR* 3.0 10.2 + - - +
298B LEU 3.8 2.1 - - - +
299B THR* 4.9 0.7 - - + -
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Residues in contact with GLU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PRO* 1.3 68.8 - - - +
119B TYR* 1.3 59.0 + - - +
120B GLU 4.1 1.0 + - - -
297B SER* 2.9 38.6 + - - +
298B LEU 3.4 6.3 - - - +
299B THR* 3.6 19.7 - - + +
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Residues in contact with TYR 119 (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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78B ASP 4.4 6.1 - - - -
79B ARG 3.1 29.8 + - - -
80B VAL 3.6 4.7 - - - -
81B PRO* 3.4 48.2 - - + +
82B GLY 5.6 0.2 - - - +
116B LEU* 4.6 11.4 - - + -
117B PRO 3.0 7.8 + - - +
118B GLU* 1.3 73.3 - - - +
120B GLU* 1.3 79.8 + - - +
121B LEU* 3.8 21.4 + - + +
122B ASP* 5.3 1.9 + - - +
296B ILE 3.4 2.1 - - - +
297B SER* 3.4 4.4 - - - -
298B LEU* 2.8 60.6 + - + +
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Residues in contact with GLU 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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78B ASP* 5.2 9.2 + - - +
79B ARG* 5.0 1.6 - - - +
118B GLU 4.1 1.2 + - - -
119B TYR* 1.3 89.3 + - - +
121B LEU* 1.3 69.9 + - - +
122B ASP* 3.5 8.9 + - - +
126B ARG* 3.1 43.9 + - - +
127B VAL* 3.6 22.1 - - + +
295B ARG* 3.4 39.5 + - + +
296B ILE 3.5 6.7 - - - +
297B SER* 4.8 2.2 - - - +
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Residues in contact with LEU 121 (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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119B TYR* 3.8 20.8 + - + +
120B GLU* 1.3 75.9 - - - +
122B ASP* 1.3 61.8 + - - +
123B LEU* 3.1 41.8 + - + +
124B PHE* 5.3 4.2 - - - -
295B ARG* 5.9 0.2 - - - -
296B ILE* 3.0 44.4 + - + +
298B LEU* 4.7 10.3 - - + -
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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