Contacts of the strand formed by residues 56 - 67 (chain E) in PDB entry 6D6Q
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 THR 56 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51E VAL* 3.7 1.6 - - - +
52E LYS* 3.3 4.7 - - - -
53E LEU* 2.9 48.7 + - + +
54E GLY 3.5 0.8 + - - -
55E HIS* 1.3 78.4 - - - +
57E ASP* 1.3 58.7 + - - +
58E ILE* 4.1 5.3 + - + +
143E GLU* 3.0 21.2 + - - -
145E GLY* 3.8 14.7 + - - -
146E GLY 4.1 15.7 + - - +
147E ASN 5.1 0.2 - - - +
148E LEU* 4.1 15.0 - - - +
151E ALA* 4.4 14.6 - - + -
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Residues in contact with ASP 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B PHE* 3.6 30.1 - - + -
50E ARG* 3.0 33.7 + - - -
51E VAL 3.3 7.3 - - - +
52E LYS* 3.8 12.5 - - + +
56E THR* 1.3 74.1 + - - +
58E ILE* 1.3 63.5 + - - +
142E LEU* 3.1 57.4 + - + +
143E GLU* 3.5 11.1 + - - +
289E PHE* 3.8 10.9 - - - -
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Residues in contact with ILE 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E ARG* 3.2 9.4 - - - +
51E VAL* 2.9 38.5 + - + +
56E THR* 4.5 9.0 - - + +
57E ASP* 1.3 80.6 - - - +
59E LEU* 1.3 75.7 + - - +
60E VAL* 4.0 12.8 - - + -
139E VAL* 4.2 11.2 - - + -
140E LEU 3.7 6.3 - - - +
141E LEU* 4.1 13.7 - - + -
142E LEU* 5.1 0.2 - - - -
143E GLU 5.5 0.2 - - - +
148E LEU* 4.0 9.2 - - + +
151E ALA* 3.4 34.1 - - + -
152E ILE* 3.4 26.9 - - + +
155E ALA* 4.3 7.2 - - + -
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Residues in contact with LEU 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B PHE* 3.7 23.1 - - + -
127B LEU* 3.7 38.4 - - + -
41E VAL* 4.4 19.1 - - + -
42E VAL* 4.4 9.0 - - + -
48E SER* 5.8 0.2 - - - -
49E ALA 3.2 19.3 - - - +
50E ARG* 3.9 19.1 - - + -
58E ILE* 1.3 74.2 - - - +
60E VAL* 1.3 75.3 + - - +
140E LEU* 2.9 44.7 + - + +
142E LEU* 4.6 9.6 - - + +
289E PHE* 5.3 4.5 - - + -
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Residues in contact with VAL 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B PHE* 5.3 0.4 - - - -
48E SER* 3.2 7.6 - - - -
49E ALA 2.9 36.3 + - - +
58E ILE* 4.0 5.8 - - + -
59E LEU* 1.3 88.3 - - - +
61E GLY* 1.3 68.2 + - - +
62E VAL* 4.2 3.4 - - + -
137E VAL* 4.3 12.1 - - + -
138E ASP 3.5 6.1 - - - +
139E VAL* 4.3 15.0 - - + -
152E ILE 4.9 1.3 - - - +
155E ALA* 3.3 39.0 - - + +
156E VAL* 4.4 3.8 - - - +
159E ALA* 3.7 24.0 - - + -
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Residues in contact with GLY 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B PHE* 4.4 26.2 - - - -
45E THR* 4.4 2.9 - - - -
47E GLY 3.7 5.2 - - - -
48E SER* 4.1 4.9 - - - -
60E VAL* 1.3 74.4 - - - +
62E VAL* 1.3 69.3 + - - +
63E LYS 4.3 0.2 - - - -
136E TYR 3.9 1.0 - - - +
137E VAL* 3.5 0.2 - - - -
138E ASP* 2.9 37.4 + - - +
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Residues in contact with VAL 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E THR* 3.6 2.5 - - - -
46E SER* 3.1 8.0 + - - -
47E GLY* 2.9 40.3 + - - +
60E VAL* 4.2 3.6 - - + -
61E GLY* 1.3 80.4 - - - +
63E LYS* 1.3 63.5 + - - +
135E LEU* 4.5 17.3 - - + -
136E TYR 3.5 6.5 - - - +
137E VAL* 4.1 22.2 - - + -
159E ALA* 3.6 31.0 - - + -
160E LEU* 4.8 7.0 - - + +
163E THR* 3.8 26.7 - - + +
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Residues in contact with LYS 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B PHE* 3.9 26.6 + - + +
82B THR 3.4 6.1 + - - -
83B GLY* 2.5 45.0 + - - -
85B ARG* 3.9 15.5 - - + +
44E ASN 4.0 13.5 + - - -
45E THR* 4.4 14.8 - - + +
46E SER* 4.4 3.4 - - - +
62E VAL* 1.3 79.2 - - - +
64E ALA* 1.3 59.4 + - - +
65E GLU* 3.6 22.6 + - + -
134E VAL 3.3 2.6 - - - +
135E LEU* 3.6 2.6 - - - -
136E TYR* 2.9 44.8 + - + +
138E ASP* 4.7 3.1 - - - +
17K MET* 5.9 1.2 - - - +
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Residues in contact with ALA 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E SER* 3.8 24.4 + - - +
63E LYS* 1.3 69.2 - - - +
65E GLU* 1.3 63.6 - - - +
133E TRP* 4.0 13.8 - - + -
134E VAL 3.4 6.3 - - - +
135E LEU* 4.0 11.4 - - + -
163E THR* 5.2 0.7 - - + -
165E ILE* 3.6 39.9 - - + -
166E PRO* 5.3 2.5 - - + +
16K VAL* 4.8 7.1 - - - +
17K MET* 6.1 0.3 - - - -
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Residues in contact with GLU 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B GLY 4.0 2.4 - - - +
84B GLU* 4.6 0.9 - - - -
85B ARG* 2.9 37.7 + - - +
63E LYS* 3.6 16.2 + - + -
64E ALA* 1.3 76.5 - - - +
66E MET* 1.3 67.7 + - - +
133E TRP* 3.3 9.5 - - - -
134E VAL* 2.9 41.7 + - + -
136E TYR* 2.9 30.7 + - + -
16K VAL 5.2 7.2 - - - +
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Residues in contact with MET 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E GLU* 1.3 76.2 - - - +
67E GLY* 1.3 58.5 + - - +
126E ILE* 4.3 13.7 - - + -
131E HIS* 4.5 17.7 - - + -
132E CYS 3.4 6.5 - - - +
133E TRP* 3.6 26.7 - - + -
134E VAL* 4.5 2.5 - - - -
168E VAL* 4.6 7.2 - - + -
170E VAL* 4.2 19.3 - - + -
180E ILE* 3.9 27.6 - - + -
14K GLY 4.7 3.8 - - - +
15K GLY* 4.3 9.6 - - - -
16K VAL* 3.5 36.1 + - + -
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Residues in contact with GLY 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E MET* 1.3 74.3 - - - +
68E THR* 1.3 65.2 + - - -
78E TYR* 5.0 1.8 - - - -
130E GLU 5.7 0.2 - - - -
131E HIS* 3.8 5.5 - - - +
132E CYS* 2.9 34.7 + - - +
134E VAL* 4.1 16.9 - - - +
136E TYR* 6.0 0.7 - - - -
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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