Contacts of the strand formed by residues 44 - 50 (chain H) in PDB entry 1JJ2
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 44 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42H TYR* 3.9 5.1 - - - +
43H PRO* 1.3 79.7 - - + +
45H GLN* 1.3 61.6 + - - +
46H VAL* 5.2 4.0 - - + -
135H TRP* 3.6 4.6 - - - -
136H VAL* 2.9 55.6 + - + +
137H ASN 4.7 5.6 - - - -
138H PRO* 4.9 5.6 - - + -
140H PRO* 5.3 5.4 - - + -
163H PRO 3.0 8.1 - - - +
164H ALA* 4.1 12.6 - - + -
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Residues in contact with GLN 45 (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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42H TYR 6.1 0.2 - - - +
44H ALA* 1.3 75.2 - - - +
46H VAL* 1.3 59.1 + - - +
47H GLU* 4.2 6.8 - - - -
86H ARG* 5.6 0.8 - - - +
133H ILE* 3.8 12.2 - - + +
134H ALA 3.4 5.8 - - - +
135H TRP* 2.8 50.8 - - + +
161H SER* 4.7 0.4 - - - -
162H SER* 2.7 60.1 + - - -
163H PRO* 3.2 26.3 + - + +
164H ALA* 4.9 0.6 - - - +
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Residues in contact with VAL 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H ALA* 5.2 3.4 - - + -
45H GLN* 1.3 76.5 - - - +
47H GLU* 1.3 59.3 + - - +
133H ILE* 3.5 2.8 - - - +
134H ALA 2.9 19.0 + - - +
136H VAL* 4.7 8.3 - - + +
140H PRO* 5.4 4.9 - - + -
142H VAL* 4.1 23.6 - - + -
143H GLU* 4.6 14.4 - - + +
146H TRP* 2.6 51.5 - - + -
159H ILE* 3.7 18.4 - - + -
160H ASP 3.1 17.5 - - - +
161H SER* 4.3 14.6 - - - +
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Residues in contact with GLU 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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45H GLN* 4.2 8.0 - - - +
46H VAL* 1.3 76.4 - - - +
48H LEU* 1.3 58.9 + - - +
49H VAL* 3.7 6.9 + - + +
86H ARG* 4.5 0.2 + - - -
130H HIS* 2.9 41.5 + - + -
132H PHE 3.2 5.4 - - - +
133H ILE* 2.9 32.0 - - + +
146H TRP* 3.0 9.4 - - - -
158H ASN 3.7 0.2 - - - +
159H ILE* 3.6 1.2 - - - -
160H ASP* 2.5 54.9 + - - +
162H SER* 2.7 25.8 + - - +
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Residues in contact with LEU 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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47H GLU* 1.3 71.7 - - - +
49H VAL* 1.3 58.1 + - - +
130H HIS* 3.3 2.3 - - - -
131H ILE* 3.0 32.3 + - + +
132H PHE* 2.8 46.8 + - + -
146H TRP* 3.6 32.1 - - + +
149H ALA* 4.0 19.5 - - + -
150H LYS* 4.1 7.6 - - + +
153H VAL* 5.4 1.1 - - + -
157H ILE* 3.2 42.8 - - + -
158H ASN 3.8 0.2 - - - -
159H ILE* 3.8 15.3 - - + -
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Residues in contact with VAL 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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47H GLU* 4.4 5.4 - - + +
48H LEU* 1.3 75.1 - - - +
50H VAL* 1.3 73.7 + - - +
51H GLU* 5.2 1.3 - - + -
128H ALA* 3.4 22.0 - - - +
129H ASN 3.4 10.1 - - - +
130H HIS* 4.1 16.8 - - + +
157H ILE* 2.7 25.2 - - - +
158H ASN* 2.8 41.6 + - + +
160H ASP* 4.2 22.7 - - + +
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Residues in contact with VAL 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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48H LEU 4.0 0.8 + - - -
49H VAL* 1.3 72.6 - - - +
51H GLU* 1.3 56.4 + - - +
52H LYS 3.0 31.6 - - - +
54H VAL* 4.5 0.7 - - + -
56H ILE* 4.6 9.0 - - + -
125H VAL* 3.7 36.3 - - + -
126H HIS 4.2 3.8 - - - +
128H ALA* 2.5 35.3 + - - -
129H ASN 3.0 8.8 + - - +
131H ILE* 4.5 15.9 - - + -
155H PRO* 4.1 21.1 - - + -
157H ILE* 4.1 15.3 - - + -
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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