Contacts of the strand formed by residues 198 - 207 (chain H) in PDB entry 6ALG
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 LEU 198 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9H LEU* 3.7 26.2 - - + -
30H PRO* 3.7 24.0 - - + -
31H LEU 3.2 20.6 - - - +
32H GLU* 4.4 7.6 - - - +
33H ARG* 4.7 6.3 - - + +
189H ALA* 3.5 9.5 - - - +
190H ALA 3.5 33.0 + - - +
192H VAL* 3.9 9.4 - - + +
195H ARG* 3.6 42.8 - - + +
197H ASP* 1.3 84.8 - - - +
199H ASP* 1.3 72.1 + - - +
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Residues in contact with ASP 199 (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 PRO* 3.5 8.8 - - - +
31H LEU* 3.0 33.3 + - + +
32H GLU 3.7 1.1 - - - +
33H ARG* 4.7 3.2 - - - +
34H GLY* 3.1 25.6 + - - -
35H PHE 3.4 1.0 + - - -
36H GLY* 2.9 30.0 + - - +
37H HIS* 5.7 0.9 - - - -
187H VAL* 3.4 25.0 - - + +
188H GLU 3.6 4.6 - - - +
189H ALA* 5.4 0.5 - - - -
190H ALA* 4.0 5.3 - - - +
198H LEU* 1.3 85.4 - - - +
200H LYS* 1.3 65.0 + - - +
201H LEU 4.1 0.4 - - - +
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Residues in contact with LYS 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H VAL* 5.7 0.9 - - - +
27H THR* 4.3 22.9 - - - +
28H LEU 3.3 9.2 - - - +
29H GLU* 3.3 39.5 + - + +
186H ASN 3.5 8.3 - - - +
187H VAL* 4.0 1.5 - - - -
188H GLU* 3.0 49.3 + - + +
189H ALA 4.9 0.9 - - - +
190H ALA* 3.7 13.7 - - + -
199H ASP* 1.3 76.9 - - - +
201H LEU* 1.3 64.1 + - - +
202H VAL* 3.3 14.7 + - + +
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Residues in contact with LEU 201 (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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231G PHE* 6.2 0.2 - - + -
26H VAL 3.7 0.7 - - - +
27H THR* 3.2 3.5 - - - -
28H LEU* 2.7 67.3 + - + +
31H LEU* 4.3 13.5 - - + +
36H GLY* 3.5 22.0 - - - +
39H LEU* 4.1 24.2 - - + +
40H GLY* 3.9 4.5 - - - +
43H LEU* 5.7 3.1 - - + -
185H TYR* 3.9 27.8 - - + -
186H ASN 4.9 0.7 - - - -
187H VAL* 4.4 7.0 - - + +
199H ASP* 4.1 2.4 - - - +
200H LYS* 1.3 70.8 - - - +
202H VAL* 1.3 61.7 + - - +
203H ILE* 3.7 24.0 - - + -
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Residues in contact with VAL 202 (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 LYS* 3.8 36.1 - - + -
26H VAL 3.4 4.5 - - - +
27H THR* 4.3 12.6 - - + +
184H ALA 4.3 0.2 - - - -
185H TYR* 3.3 21.3 - - - -
186H ASN* 3.4 29.0 + - + +
188H GLU* 4.2 20.4 - - - +
200H LYS* 3.3 21.7 + - + +
201H LEU* 1.3 75.8 - - - +
203H ILE* 1.3 62.5 + - - +
204H GLU* 3.6 5.2 + - + +
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Residues in contact with ILE 203 (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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24H ALA 4.7 0.2 - - - -
25H LYS* 3.3 2.1 - - - +
26H VAL* 2.5 55.3 + - + +
28H LEU* 5.3 3.8 - - + -
40H GLY* 4.6 9.2 - - - +
43H LEU* 5.0 19.1 - - + -
47H LEU* 5.5 5.6 - - + -
183H ILE* 5.7 2.9 - - + -
184H ALA 3.8 4.3 - - - +
185H TYR* 3.8 18.2 - - + -
201H LEU* 3.7 35.9 - - + +
202H VAL* 1.3 72.0 - - - +
204H GLU* 1.3 65.9 + - - +
205H MET* 4.9 4.0 - - + -
217H ILE* 3.8 28.5 - - + -
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Residues in contact with GLU 204 (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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23H HIS* 3.6 24.9 + - + +
24H ALA 3.6 12.3 - - - +
25H LYS* 4.6 21.9 + - + +
182H ARG* 3.7 26.7 + - - +
183H ILE* 3.4 5.7 - - - +
184H ALA* 3.2 38.3 + - + +
186H ASN* 5.1 8.8 + - - -
202H VAL* 4.6 6.0 - - + +
203H ILE* 1.3 74.6 - - - +
205H MET* 1.3 62.2 + - - +
206H GLU* 5.9 0.4 - - + -
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Residues in contact with MET 205 (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 THR 3.7 1.0 - - - +
23H HIS 3.7 0.7 - - - -
24H ALA* 3.0 40.0 + - + +
47H LEU* 3.7 24.9 - - - -
180H VAL* 3.7 27.4 - - + -
182H ARG 3.3 4.0 - - - +
183H ILE* 3.6 13.0 - - + -
203H ILE* 4.2 6.5 - - + -
204H GLU* 1.3 76.5 - - - +
206H GLU* 1.3 72.0 + - - +
207H THR* 4.3 2.0 - - + -
213H PRO* 3.2 39.4 - - + +
216H ALA* 3.7 17.5 - - + -
217H ILE* 3.7 18.6 - - + -
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Residues in contact with GLU 206 (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 THR* 3.3 12.3 - - + +
23H HIS* 2.7 45.0 + - + +
180H VAL* 3.8 1.0 - - - +
181H GLU* 2.8 28.8 + - + +
182H ARG* 3.0 34.8 + - + +
204H GLU* 5.3 0.6 - - + +
205H MET* 1.3 75.2 - - - +
207H THR* 1.3 65.1 + - - +
531J LYS* 2.9 37.0 + - - +
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Residues in contact with THR 207 (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 THR* 2.4 36.3 + - - +
179H PRO 3.3 15.5 - - - +
180H VAL* 4.0 7.6 - - + +
181H GLU* 4.6 10.2 - - - +
205H MET* 4.3 13.2 - - + -
206H GLU* 1.3 78.9 - - - +
208H ASN* 1.3 61.0 + - - +
209H GLY* 3.3 6.6 + - - -
211H ILE* 3.3 25.2 + - + +
213H PRO* 3.8 30.0 - - + +
216H ALA* 4.7 6.1 - - + -
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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