Contacts of the strand formed by residues 46 - 56 (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 TRP 46 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36H VAL* 3.7 23.1 - - + -
37H SER* 3.4 7.4 - - - -
38H LYS* 3.3 40.6 - - + -
39H ASP 3.7 0.6 + - - +
42H ARG* 3.2 18.5 - - - +
44H THR* 3.2 25.2 + - - -
45H GLY* 1.3 88.4 + - - +
47H SER* 1.3 60.6 + - - +
48H VAL* 4.2 2.4 + - - +
127H HIS* 5.6 1.7 - - - +
128H LEU* 6.1 1.2 - - - +
133H LEU* 4.0 19.8 - - + +
150H GLU 5.5 1.1 - - - -
151H LEU* 3.6 26.0 - - + -
154H ALA* 3.6 18.2 - - + -
155H PHE* 3.1 36.7 - + - -
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Residues in contact with SER 47 (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* 3.3 1.9 - - - +
36H VAL* 3.2 6.9 - - - +
37H SER* 2.8 49.9 + - - -
39H ASP* 4.0 9.3 - - - +
42H ARG* 3.8 31.0 - - - +
46H TRP* 1.3 72.5 - - - +
48H VAL* 1.3 61.7 + - - +
49H ARG* 6.0 2.4 - - - -
5J T 5.9 4.5 - - - -
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Residues in contact with VAL 48 (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* 5.1 4.0 - - + -
35H THR 3.3 3.6 - - - +
36H VAL* 3.7 21.8 - - + -
46H TRP 4.2 2.1 + - - +
47H SER* 1.3 78.5 - - - +
49H ARG* 1.3 67.2 + - - +
50H PRO* 4.6 1.0 - - - +
122H ILE* 3.9 20.3 - - + +
127H HIS* 4.3 25.4 + - + +
133H LEU* 3.6 31.2 - - + -
136H ILE* 3.7 35.0 - - + -
4J A 5.3 1.7 + - - -
5J T 5.5 2.4 - - - +
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Residues in contact with ARG 49 (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* 3.5 6.8 - - - +
35H THR* 2.9 53.2 + - - +
47H SER* 5.9 2.5 - - - +
48H VAL* 1.3 77.4 - - - +
50H PRO* 1.3 72.5 + - + +
51H ARG* 3.7 28.2 - - - +
87H GLU* 3.2 31.9 + - - +
122H ILE* 4.6 0.2 - - - -
5J T 3.9 41.3 - - + +
6J G 2.6 41.8 + - - -
7J C 4.0 0.4 - - - +
21K G 3.6 12.2 + - - -
22K C 4.1 5.5 - - - +
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Residues in contact with PRO 50 (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 3.5 6.3 - - - +
34H LEU* 3.8 10.3 - - + -
49H ARG* 1.3 92.8 + - + +
51H ARG* 1.3 66.2 + - - +
87H GLU* 3.9 15.9 - - - +
89H LEU* 5.0 4.7 - - + -
92H LEU* 3.5 24.3 - - + +
115H PHE* 3.4 23.8 - - + -
119H PHE* 4.5 13.7 - - + -
122H ILE* 3.7 28.5 - - + -
5J T 5.7 2.7 - - - +
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Residues in contact with ARG 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H SER 4.5 0.7 - - - -
32H PHE* 3.6 1.2 - - - -
33H MET* 2.9 65.1 + - + +
35H THR* 2.8 31.8 + - - -
49H ARG* 3.7 20.3 - - + +
50H PRO* 1.3 81.3 - - - +
52H PHE* 1.3 60.8 + - - +
53H ARG* 4.5 7.3 - - + +
86H PHE 3.6 7.6 - - - +
87H GLU* 3.0 33.1 + - + +
115H PHE* 3.3 11.7 - - - -
7J C 3.2 6.1 - - - +
8J T 4.6 0.2 + - - -
19K G 6.0 0.4 + - - -
20K A 3.6 19.3 + - - +
21K G 2.9 44.6 + - - -
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Residues in contact with PHE 52 (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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26H ALA* 4.3 0.7 - - + -
30H SER* 3.6 32.5 - - - -
31H SER 3.5 5.2 - - - -
32H PHE* 3.3 45.3 - + + -
51H ARG* 1.3 75.1 - - - +
53H ARG* 1.3 67.6 + - - +
54H ILE* 4.1 20.2 - - + -
85H ARG* 3.5 1.4 - - - +
86H PHE* 2.9 63.3 + + + -
87H GLU* 5.5 0.2 - - - +
92H LEU* 3.7 18.8 - - + +
95H VAL* 3.9 17.5 - - + -
99H PHE* 3.8 18.6 - + - -
115H PHE* 4.8 0.2 - - + -
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Residues in contact with ARG 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H ASP 4.7 0.3 - - - +
30H SER* 3.4 4.0 - - - -
31H SER* 2.9 36.3 + - - +
33H MET* 3.5 32.5 - - + +
51H ARG* 4.5 7.6 - - + +
52H PHE* 1.3 78.7 - - - +
54H ILE* 1.3 75.1 + - - +
55H GLY* 4.3 0.6 - - - +
83H ARG* 3.0 38.8 - - + +
84H ILE 3.4 14.4 - - - +
85H ARG* 4.2 16.2 - - + +
87H GLU* 5.1 4.2 + - - -
8J T 4.8 2.8 + - - -
18K G 2.9 24.7 + - - -
19K G 2.8 42.0 + - - -
20K A 4.3 8.7 - - - +
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Residues in contact with ILE 54 (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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22H ILE* 5.7 2.7 - - + +
25H PHE* 4.3 12.8 - - + +
26H ALA* 4.4 13.0 - - + +
29H ASP* 4.8 6.5 - - + -
30H SER* 3.5 20.4 - - - +
52H PHE* 4.1 20.8 - - + -
53H ARG* 1.3 82.2 - - - +
55H GLY* 1.3 61.8 + - - +
56H LEU* 4.1 17.7 - - + -
64H LEU* 4.0 17.5 - - + +
67H ILE* 4.1 26.2 - - + -
82H ALA 3.9 0.3 - - - +
83H ARG* 3.2 4.2 - - - +
84H ILE* 2.9 47.2 + - + +
86H PHE* 5.7 0.4 - - + -
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Residues in contact with GLY 55 (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* 4.3 3.9 + - - +
53H ARG* 4.3 1.6 - - - +
54H ILE* 1.3 73.3 - - - +
56H LEU* 1.3 68.8 + - - +
81H ASP* 5.2 4.3 - - - -
82H ALA 3.3 7.0 - - - -
83H ARG* 4.2 11.2 - - - -
16K T 2.4 41.9 + - - -
17K A 6.4 0.4 - - - -
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Residues in contact with LEU 56 (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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25H PHE* 3.5 37.2 - - + -
29H ASP* 3.3 24.0 - - + +
54H ILE* 4.1 8.3 - - + -
55H GLY* 1.3 90.7 - - - +
57H HIS* 1.3 68.0 + - - +
60H ASP* 4.1 26.5 - - + +
63H ILE* 4.2 6.1 - - + -
64H LEU* 3.7 23.6 - - + -
81H ASP* 3.5 8.8 - - - +
82H ALA* 2.8 34.4 + - + +
16I T 4.2 5.4 - - - -
16K T 3.9 5.8 - - - +
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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