Contacts of the strand formed by residues 24 - 31 (chain K) in PDB entry 6XAV
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 24 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17K GLU 3.8 7.0 - - - +
18K GLN* 3.8 10.3 - - - +
19K VAL* 5.2 1.3 - - - -
22K THR 3.6 4.2 + - - +
23K HIS* 1.3 89.3 - - - +
25K LYS* 1.3 65.5 + - - +
26K VAL* 5.1 0.4 - - + -
204K GLU* 3.5 7.3 - - - +
205K MET* 3.4 33.0 + - + +
213K PRO* 3.7 31.4 - - + -
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Residues in contact with LYS 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K ASP 4.4 0.3 - - - +
16K ILE* 3.6 0.5 - - - -
17K GLU* 2.7 68.1 + - + +
19K VAL* 5.2 5.6 - - + -
23K HIS* 5.1 4.3 - - - -
24K ALA* 1.3 78.1 - - - +
26K VAL* 1.3 59.7 + - - +
27K THR* 4.9 2.6 + - - +
202K VAL* 3.8 27.6 - - + +
203K ILE 3.4 7.4 - - - +
204K GLU* 3.1 40.1 + - + +
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Residues in contact with VAL 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K LEU* 3.7 22.4 - - + -
15K ASP 3.6 12.3 - - - +
16K ILE* 3.7 11.9 - - + +
25K LYS* 1.3 79.3 - - - +
27K THR* 1.3 75.2 + - - +
28K LEU* 4.4 3.8 - - + -
202K VAL* 3.3 5.9 - - - +
203K ILE* 2.6 40.2 + - + +
205K MET* 4.3 10.1 - - + -
213K PRO* 4.1 24.5 - - + -
217K ILE* 3.7 33.7 - - + -
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Residues in contact with THR 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K ARG 4.0 0.3 - - - +
13K LEU* 4.2 4.7 - - - +
14K VAL* 3.6 27.1 + - + -
15K ASP* 3.2 25.2 + - - +
25K LYS* 4.9 2.9 + - - +
26K VAL* 1.3 81.3 + - - +
28K LEU* 1.3 74.2 + - - +
29K GLU* 4.1 7.0 - - + +
200K LYS* 4.5 19.3 - - + +
201K LEU 3.2 7.6 - - - +
202K VAL* 4.3 21.2 - - + +
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Residues in contact with LEU 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228H LEU* 6.5 0.2 - - + -
231H PHE* 3.5 39.7 - - + -
11K PRO* 4.8 7.9 - - + -
12K ARG 4.0 3.4 - - - -
13K LEU* 5.5 0.4 - - + -
26K VAL* 4.4 2.5 - - + -
27K THR* 1.3 84.7 - - - +
29K GLU* 1.3 58.4 + - - +
31K LEU* 3.6 10.8 - - + +
39K LEU* 5.8 6.1 - - + -
43K LEU* 3.9 26.2 - - + -
200K LYS 3.6 0.2 - - - -
201K LEU* 2.5 62.7 + - + +
203K ILE* 4.0 20.0 - - + -
217K ILE* 4.3 16.8 - - + -
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Residues in contact with GLU 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K PRO* 3.9 0.2 - - - -
12K ARG* 2.6 41.4 + - - +
14K VAL* 3.8 18.6 - - + +
27K THR* 4.1 5.6 - - + +
28K LEU* 1.3 75.4 - - - +
30K PRO* 1.4 87.0 - - + +
31K LEU 4.2 0.2 - - - +
190K ALA* 3.0 28.7 - - + +
191K ARG 4.4 0.7 + - - -
193K GLU* 3.9 23.1 - - - +
198K LEU* 5.4 1.3 - - + +
199K ASP 4.4 2.9 - - - +
200K LYS* 3.4 31.8 + - + +
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Residues in contact with PRO 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K LEU* 3.4 30.6 - - + +
10K LYS 3.5 19.5 - - - +
11K PRO* 3.3 13.7 - - + +
12K ARG* 4.2 6.3 - - + +
29K GLU* 1.4 99.4 - - + +
31K LEU* 1.3 70.1 + - - +
193K GLU* 6.5 0.2 - - + -
198K LEU* 4.8 20.4 - - + -
199K ASP 4.2 0.2 - - - +
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Residues in contact with LEU 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227H GLN* 5.6 0.9 - - - +
9K LEU 4.8 1.6 - - - +
11K PRO* 3.6 26.9 - - + -
28K LEU* 3.6 11.7 - - + +
30K PRO* 1.3 83.6 - - - +
32K GLU* 1.3 68.4 + - - +
35K PHE* 4.1 6.5 - - + +
36K GLY* 3.7 28.0 - - - +
39K LEU* 4.2 14.1 - - + -
187K VAL* 5.5 0.2 - - + -
198K LEU* 3.5 10.8 - - - +
199K ASP* 2.8 44.4 + - + +
200K LYS 4.4 1.1 - - - -
201K LEU* 3.5 38.4 - - + +
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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