Contacts of the strand formed by residues 12 - 22 (chain H) in PDB entry 6B0B
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 MET 12 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7H ILE 4.5 10.5 - - - +
8H ILE* 4.7 3.1 - - + -
9H LYS* 3.4 37.0 - - - +
10H GLU 4.3 0.2 - - - -
11H PHE* 1.3 85.0 - - - +
13H ARG* 1.3 68.1 + - - +
34H GLU* 3.6 1.6 - - - -
35H GLY 3.2 30.2 + - - +
37H PRO* 4.6 12.5 - - + +
72H TYR* 3.9 7.6 + - - +
118H PHE* 3.5 45.3 - - + +
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Residues in contact with ARG 13 (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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11H PHE* 4.0 20.8 - - + -
12H MET* 1.3 78.2 - - - +
14H PHE* 1.3 64.7 + - - +
32H GLU* 6.3 0.8 - - - +
33H GLY 3.3 15.5 + - - +
34H GLU* 2.4 46.5 + - + +
118H PHE* 3.2 27.9 + - - -
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Residues in contact with PHE 14 (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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13H ARG* 1.3 77.7 - - - +
15H LYS* 1.3 72.4 + - - +
16H VAL* 4.1 19.7 - - + -
32H GLU* 3.4 6.1 - - - +
33H GLY* 3.1 57.2 + - - +
34H GLU* 4.0 2.9 - - - -
42H GLN* 3.9 22.9 - - - -
43H THR 4.3 1.8 - - - -
44H ALA* 3.8 19.7 - - + -
65H PHE* 5.2 10.5 - + + -
72H TYR* 3.1 25.1 - + - +
118H PHE* 3.5 25.1 - - + +
120H TYR* 3.6 28.9 - + + -
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Residues in contact with LYS 15 (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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14H PHE* 1.3 80.1 - - - +
16H VAL* 1.3 61.6 + - - +
31H GLY 3.4 7.2 - - - +
32H GLU* 4.5 13.9 - - + -
118H PHE 2.8 15.1 + - - +
119H ILE* 3.4 22.5 - - + +
120H TYR* 2.9 26.5 + - - +
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Residues in contact with VAL 16 (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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14H PHE* 4.1 14.1 - - + -
15H LYS* 1.3 75.9 - - - +
17H HIS* 1.3 64.0 + - - +
18H MET* 4.7 3.4 - - + +
29H ILE* 3.8 2.4 - - + +
30H GLU* 3.5 7.3 - - - +
31H GLY* 2.9 55.6 + - - +
46H LEU* 4.2 13.0 - - + -
65H PHE* 4.1 18.4 - - + -
120H TYR* 3.5 30.3 - - + -
122H VAL* 3.9 18.8 - - + -
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Residues in contact with HIS 17 (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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16H VAL* 1.3 73.2 - - - +
18H MET* 1.3 69.1 + - - +
19H GLU* 4.4 6.9 - - + +
28H GLU* 3.2 31.1 + - + -
30H GLU* 2.6 35.0 + - - +
119H ILE* 6.5 0.2 - - + -
120H TYR 2.9 11.6 + - - +
121H LYS* 3.4 34.5 + - + -
122H VAL* 2.9 23.6 + - - +
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Residues in contact with MET 18 (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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16H VAL* 4.2 3.1 - - + -
17H HIS* 1.3 77.9 - - - +
19H GLU* 1.3 69.7 + - - +
20H GLY 4.2 0.6 + - - +
27H PHE* 4.6 7.9 - - + -
28H GLU* 3.2 7.1 - - - +
29H ILE* 2.9 62.9 + - + +
61H LEU* 4.7 8.7 - - + +
64H GLN* 4.8 12.6 - - + -
65H PHE* 4.5 24.0 - - + -
122H VAL* 3.4 41.3 - - + +
124H LEU* 4.3 27.1 - - + -
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Residues in contact with GLU 19 (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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17H HIS* 4.3 10.0 - - + +
18H MET* 1.3 74.6 - - - +
20H GLY* 1.3 59.1 + - - +
27H PHE 3.7 4.3 - - - +
28H GLU* 4.2 15.3 - - + -
121H LYS* 5.9 3.4 - - - +
122H VAL 2.9 10.3 + - - +
123H LYS* 3.2 12.7 - - + +
124H LEU 2.9 21.8 + - - +
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Residues in contact with GLY 20 (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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18H MET 4.1 0.8 - - - -
19H GLU* 1.3 75.9 - - - +
21H SER* 1.3 61.4 + - - -
26H GLU* 3.4 4.5 - - - +
27H PHE* 2.9 56.8 + - - +
124H LEU* 3.1 15.7 - - - -
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Residues in contact with SER 21 (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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20H GLY* 1.3 75.2 - - - -
22H VAL* 1.3 62.2 + - - +
24H GLY* 4.7 7.6 + - - -
25H HIS 3.3 7.4 - - - -
26H GLU* 4.0 21.3 - - - -
27H PHE* 3.8 1.2 - - - -
124H LEU* 2.9 13.1 + - - +
125H ARG* 3.3 14.9 - - - +
126H GLY 2.9 23.0 + - - +
127H THR* 5.5 0.2 - - - +
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Residues in contact with VAL 22 (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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21H SER* 1.3 73.8 - - - +
23H ASN* 1.3 83.2 + - + +
24H GLY 3.1 0.2 - - - -
25H HIS* 2.9 30.2 + - - +
27H PHE* 3.6 19.7 - - + -
55H PRO* 5.6 1.0 - - - +
56H PHE* 3.6 45.9 - - + -
60H ILE* 4.9 4.7 - - + -
124H LEU* 3.8 18.6 - - + -
126H GLY* 3.2 10.1 - - - +
129H PHE* 4.4 15.9 - - + -
136H MET* 4.9 4.0 - - + +
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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