Contacts of the strand formed by residues 61 - 68 (chain K) in PDB entry 1A81
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 61 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184I ILE* 5.5 5.4 - - + +
26K GLU* 3.7 34.6 - - + +
29K LEU* 4.2 12.3 - - + -
34K MET* 3.9 15.5 - - + +
55K VAL 3.9 3.4 - - - -
60K LYS* 1.3 76.7 - - - +
62K HIS* 1.3 71.2 + - - +
63K HIS* 4.2 10.5 + - + +
182L SER* 4.7 1.6 + - - -
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Residues in contact with HIS 62 (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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53K LEU 3.2 2.1 - - - +
54K SER* 3.0 5.8 - - - -
55K VAL* 2.8 58.8 + - + +
57K HIS* 3.0 44.1 + + + +
60K LYS* 4.2 9.9 + - + +
61K ALA* 1.3 81.0 + - - +
63K HIS* 1.3 63.0 + - - +
64K TYR* 3.9 8.1 + - + -
100K VAL* 4.0 27.8 - - + +
182L SER* 3.6 14.4 + - - +
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Residues in contact with HIS 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22K ARG* 3.2 56.1 - - - +
25K ALA* 4.4 1.8 - - + -
26K GLU* 3.4 29.5 - - + +
42K ARG* 2.8 30.9 + - - +
52K ALA* 6.0 0.4 - - + -
53K LEU 3.2 1.3 + - - -
54K SER* 3.4 25.9 - - - -
61K ALA* 4.6 9.9 - - + +
62K HIS* 1.3 74.5 - - - +
64K TYR* 1.3 63.3 + - - +
65K THR 4.2 0.5 + - - -
181L PTR 4.1 13.6 - - + +
182L SER* 3.0 36.2 + - - +
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Residues in contact with TYR 64 (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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52K ALA* 3.0 5.8 - - - +
53K LEU* 2.5 59.4 + - + +
55K VAL* 4.7 7.0 - - + -
62K HIS* 4.4 20.0 - - + -
63K HIS* 1.3 75.9 - - - +
65K THR* 1.3 61.5 + - - +
66K ILE 3.8 0.7 + - - -
76K ILE* 4.3 27.6 - - + -
98K GLY 4.2 1.9 + - - -
99K LEU* 3.4 34.1 - - + -
100K VAL* 3.2 32.1 + - + +
181L PTR 5.0 0.9 - - - -
182L SER* 3.0 40.1 - - - -
183L GLY* 2.8 28.5 + - - -
184L LEU* 3.9 4.9 - - + -
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Residues in contact with THR 65 (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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44K SER* 3.9 13.1 + - - -
46K ASN* 5.3 1.5 + - - -
47K TYR* 3.7 26.7 - - + +
51K PHE 3.4 7.8 + - - -
52K ALA* 4.4 1.3 - - - +
63K HIS 4.2 0.6 + - - -
64K TYR* 1.3 74.2 - - - +
66K ILE* 1.3 65.1 + - - +
67K GLU* 3.6 17.3 + - - +
76K ILE* 3.6 22.4 - - + +
77K ALA* 4.3 2.3 + - + +
181L PTR 4.3 26.9 - - + -
182L SER 5.2 2.4 + - - +
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Residues in contact with ILE 66 (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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41K LEU* 4.2 17.9 - - + -
44K SER* 5.4 0.2 - - - -
47K TYR* 5.8 0.3 - - - +
50K GLY* 3.1 5.0 - - - -
51K PHE* 2.5 72.3 + - + +
53K LEU* 4.2 16.6 - - + -
64K TYR 4.8 2.5 - - - +
65K THR* 1.3 69.9 + - - +
67K GLU* 1.3 60.2 + - - +
74K TYR* 3.7 28.7 - - + -
75K ALA 4.4 3.4 - - - +
76K ILE* 3.9 23.8 - - + +
85K PRO* 5.2 9.2 - - + -
88K LEU* 4.0 23.1 - - + -
89K CYS* 5.6 3.1 - - - -
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Residues in contact with GLU 67 (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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47K TYR* 3.2 41.4 + - + -
50K GLY* 4.5 2.5 - - - -
65K THR* 3.6 17.2 + - - +
66K ILE* 1.3 74.8 - - - +
68K ARG* 1.3 62.6 + - - +
69K GLU* 3.6 6.0 + - - +
74K TYR* 3.3 3.3 - - - -
75K ALA 2.9 39.7 + - - +
77K ALA* 4.2 21.4 - - - +
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Residues in contact with ARG 68 (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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48K LEU 4.4 8.5 + - - +
49K GLY* 3.8 18.6 + - - +
50K GLY* 4.2 2.4 - - - -
66K ILE 4.0 1.0 + - - -
67K GLU* 1.3 72.9 - - - +
69K GLU* 1.3 79.3 + - - +
70K LEU* 3.6 4.1 + - - +
72K GLY* 2.8 39.0 + - - -
74K TYR* 3.5 45.1 + - + -
152K PRO* 3.5 51.4 + - - +
155K GLU* 3.7 15.1 + - - +
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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