Contacts of the strand formed by residues 30 - 38 (chain H) in PDB entry 6BCH
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 SER 30 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26H ALA* 2.6 36.1 + - - +
28H ALA 3.8 1.3 - - - +
29H ASP* 1.3 81.7 - - - +
31H SER* 1.3 61.2 + - - +
32H PHE* 4.4 8.5 - - - -
52H PHE* 3.6 17.4 - - - -
53H ARG 3.4 6.7 - - - -
54H ILE* 3.5 26.0 - - - -
104H LEU* 5.2 1.0 - - - +
108H LYS* 5.6 6.6 - - - +
17K A 4.8 1.3 - - - +
18K G 3.5 13.0 + - - -
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Residues in contact with SER 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29H ASP 5.4 0.2 - - - -
30H SER* 1.3 76.6 - - - +
32H PHE* 1.3 66.0 + - - +
33H MET* 3.6 30.3 + - - +
51H ARG 4.0 0.3 - - - +
52H PHE* 3.5 6.1 - - - -
53H ARG* 2.9 38.2 + - - -
144H ASN* 3.8 8.4 + - - -
17K A 4.8 8.3 - - - -
18K G 3.7 27.4 + - - +
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Residues in contact with PHE 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H SER* 4.4 7.2 - - - -
31H SER* 1.3 74.3 + - - +
33H MET* 1.3 56.7 + - - +
51H ARG 3.6 2.2 - - - -
52H PHE* 3.3 39.3 - + + -
95H VAL* 4.5 3.1 - - + -
99H PHE* 3.8 14.4 - + - -
104H LEU* 3.8 21.1 - - + -
108H LYS* 4.3 13.5 - - + -
111H ASP* 4.8 5.4 - - + +
112H TYR* 3.4 43.1 - + + -
115H PHE* 3.7 37.9 - + + -
143H LEU* 3.8 13.6 - - + +
144H ASN* 2.5 36.1 + - - +
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Residues in contact with MET 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H SER* 3.6 25.1 - - - +
32H PHE* 1.3 77.2 - - - +
34H LEU* 1.3 64.9 + - - +
35H THR* 4.2 1.1 - - - +
49H ARG 4.6 0.2 - - - -
50H PRO* 3.5 3.8 - - - +
51H ARG* 2.9 62.1 + - + +
53H ARG* 3.5 58.8 - - + +
115H PHE* 3.6 6.4 - - - -
143H LEU* 4.1 3.1 - - - -
144H ASN* 4.3 0.9 - - - +
18K G 4.4 3.8 - - - -
19K G 3.7 35.2 - - + +
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Residues in contact with LEU 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H MET* 1.3 81.6 - - - +
35H THR* 1.3 60.5 + - - +
36H VAL* 5.3 2.9 - - + -
48H VAL* 5.1 4.7 - - + -
49H ARG 3.5 4.3 - - - +
50H PRO* 3.8 23.6 - - + -
114H LEU 5.5 0.2 - - - -
115H PHE* 4.5 10.3 - - + +
118H ALA* 3.6 34.1 - - + -
122H ILE* 4.3 7.2 - - + -
136H ILE* 4.4 9.4 - - + +
139H LEU* 4.7 2.9 - - + -
140H LYS* 2.5 65.4 + - + +
143H LEU* 3.8 25.7 - - + +
19K G 5.3 1.2 + - - -
20K A 4.7 0.5 + - - -
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Residues in contact with THR 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H MET* 4.2 2.0 - - - +
34H LEU* 1.3 72.7 - - - +
36H VAL* 1.3 63.4 + - - +
37H SER* 3.7 22.0 - - - +
47H SER* 3.3 2.0 - - - +
48H VAL* 3.3 6.4 - - - +
49H ARG* 2.9 45.8 + - + +
51H ARG* 2.8 42.2 + - - +
140H LYS* 4.8 0.4 - - - +
20K A 4.2 23.1 + - + +
21K G 4.3 7.9 - - - +
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Residues in contact with VAL 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H LEU* 3.9 2.6 + - + +
35H THR* 1.3 77.0 - - - +
37H SER* 1.3 61.3 + - - +
46H TRP* 3.7 33.1 - - + -
47H SER 3.2 7.2 - - - +
48H VAL* 3.7 25.6 - - + -
133H LEU* 4.7 0.7 - - + -
136H ILE* 5.0 4.5 - - + -
137H LEU* 4.4 21.8 - - + -
140H LYS* 3.9 24.5 - - + +
151H LEU* 4.0 28.2 - - + +
155H PHE* 5.1 0.9 - - + -
20K A 5.4 1.4 + - - -
21K G 5.0 2.6 + - - -
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Residues in contact with SER 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H THR* 3.7 20.4 - - - +
36H VAL* 1.3 71.8 + - - +
38H LYS* 1.3 66.6 + - - +
46H TRP* 3.4 5.9 - - - -
47H SER* 2.8 46.7 + - - -
20K A 4.3 0.7 - - - +
21K G 3.5 41.3 + - - -
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Residues in contact with LYS 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A TYR* 5.5 6.1 - - - +
37H SER* 1.3 74.8 - - - +
39H ASP* 1.3 61.2 + - - +
45H GLY 3.7 3.8 - - - +
46H TRP* 3.3 32.4 - - + -
21K G 5.3 1.4 + - - -
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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