Contacts of the strand formed by residues 57 - 68 (chain B) in PDB entry 4DAY
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 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B PRO* 3.5 37.2 - - + -
20B SER* 4.0 15.6 + - - +
21B PRO 3.6 5.2 - - - +
22B PRO* 3.3 6.9 - - + +
23B LEU* 3.3 15.2 + - - +
56B ALA* 1.3 78.4 + - + +
58B VAL* 1.3 64.8 + - - +
105B MET* 4.9 5.8 - - + -
106B GLY 3.6 7.4 - - - +
107B VAL* 4.5 4.9 - - + +
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Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PRO* 3.7 4.0 - - - -
23B LEU* 3.4 15.3 - - + +
25B VAL* 3.6 24.5 - - + -
30B LEU* 4.8 3.8 - - + -
56B ALA 4.9 4.0 - - - +
57B ALA* 1.3 80.5 - - - +
59B TRP* 1.3 61.1 + - - +
60B MET* 4.2 14.1 - - + -
104B VAL 3.6 0.4 - - - +
105B MET* 3.2 12.0 - - - +
106B GLY 2.8 43.0 + - - +
108B VAL* 3.8 20.9 - - + -
117B LEU* 3.6 23.1 - - + -
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Residues in contact with TRP 59 (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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511A LYS* 3.9 41.3 - - - -
512A ALA* 4.7 0.9 - - - -
513A PHE* 3.5 37.5 - + + -
536A ASP* 3.6 24.0 - - - -
537A GLY* 4.1 15.3 - - - -
589A CYS* 4.5 4.7 - - - -
22B PRO* 3.7 9.4 - - + -
23B LEU 2.6 28.2 + - - +
24B LYS* 3.2 20.6 - - + -
25B VAL 3.1 14.6 + - - -
58B VAL* 1.3 72.7 - - - +
60B MET* 1.3 67.2 + - - +
61B GLN* 3.3 20.4 + - - +
103B MET* 3.5 23.6 - - + +
104B VAL 3.4 4.7 - - - -
105B MET* 4.7 0.4 - - - +
135B TRP* 3.3 18.9 - + - -
138B GLU* 4.4 0.4 - - - -
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Residues in contact with MET 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL* 3.5 18.4 - - + +
26B LEU* 3.6 7.2 - - - -
27B ALA* 3.4 37.0 - - - +
30B LEU* 3.7 22.4 - - + -
58B VAL* 4.3 5.2 - - + -
59B TRP* 1.3 77.0 - - - +
61B GLN* 1.3 64.1 + - - +
76B ASP* 4.3 0.9 - - - +
81B PHE* 3.6 35.4 - - + -
102B VAL 4.1 0.2 - - - +
103B MET* 3.4 2.4 - - - +
104B VAL* 2.7 42.1 + - + +
115B PRO* 5.4 1.6 - - + -
117B LEU* 3.5 28.3 - - + -
135B TRP* 3.9 5.6 - - - -
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Residues in contact with GLN 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A LYS* 4.1 7.8 + - - -
589A CYS* 5.2 0.2 - - - -
59B TRP* 3.3 18.6 + - - +
60B MET* 1.3 80.8 - - - +
62B GLY* 1.3 59.6 + - - +
76B ASP* 3.0 22.7 + - - +
81B PHE* 3.3 15.9 - - - -
101B TYR* 3.1 33.3 + - + +
102B VAL 3.3 8.5 - - - +
103B MET* 3.5 13.3 - - + +
125B LEU* 3.6 18.1 - - - +
131B HIS* 3.9 5.5 + - - +
135B TRP* 3.3 42.4 - - + +
138B GLU* 3.9 7.8 + - - +
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Residues in contact with GLY 62 (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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61B GLN* 1.3 79.7 - - - +
63B ARG* 1.3 66.5 + - - -
74B LEU* 3.3 14.3 - - - +
75B ARG 3.2 18.2 - - - -
76B ASP* 3.9 2.0 - - - -
81B PHE* 4.6 0.2 - - - -
101B TYR* 3.7 16.9 - - - -
102B VAL 3.2 23.6 + - - +
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Residues in contact with ARG 63 (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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62B GLY* 1.3 72.6 - - - -
64B VAL* 1.3 64.2 + - - +
65B VAL* 3.9 0.2 - - - +
74B LEU* 3.2 3.9 - - - -
75B ARG* 2.7 72.7 + - + +
99B GLY* 3.4 32.6 + - - -
100B LYS 3.3 7.3 + - - -
101B TYR* 3.7 22.0 - - + +
129B PRO* 6.2 1.4 - - - +
132B GLU* 2.9 37.9 + - - +
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Residues in contact with VAL 64 (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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63B ARG* 1.3 73.6 - - - +
65B VAL* 1.3 61.1 + - - +
66B MET 4.0 17.7 - - - +
67B ALA* 4.0 12.6 - - + -
72B ALA* 4.8 2.7 - - + -
73B ARG 4.5 1.6 - - - +
74B LEU* 3.7 20.4 - - + -
96B LEU* 3.7 26.5 - - + -
97B VAL 3.4 23.1 - - - +
98B PRO* 3.4 9.4 - - + +
99B GLY* 2.9 22.3 + - - -
100B LYS* 2.8 26.6 + - + +
102B VAL* 4.4 6.3 - - + -
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Residues in contact with VAL 65 (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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64B VAL* 1.3 74.7 - - - +
66B MET* 1.3 68.4 + - + +
73B ARG* 2.9 39.5 + - - +
74B LEU 3.7 3.6 - - - +
75B ARG* 3.5 41.3 - - + +
80B ASP* 4.5 9.9 - - - +
98B PRO* 3.8 14.3 - - - +
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Residues in contact with MET 66 (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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64B VAL* 4.0 3.2 - - - +
65B VAL* 1.3 85.4 - - + +
67B ALA* 1.3 60.0 + - - +
68B ASP* 4.3 1.8 - - + -
71B GLU* 5.7 1.3 - - - +
72B ALA* 3.1 6.0 - - - +
73B ARG* 2.8 70.4 + - + +
98B PRO* 5.1 2.5 - - - -
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B VAL* 4.0 13.4 - - + +
66B MET* 1.3 76.6 - - - +
68B ASP* 1.3 74.2 + - - +
71B GLU 3.8 5.8 - - - +
72B ALA* 3.9 4.7 - - + +
96B LEU* 3.1 40.9 - - + +
98B PRO* 4.8 10.1 - - + +
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Residues in contact with ASP 68 (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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66B MET* 6.3 1.3 - - + -
67B ALA* 1.3 85.9 - - - +
69B ARG* 1.3 73.6 + - + +
70B GLY 3.3 0.5 + - - -
71B GLU* 2.8 43.4 + - - +
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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