Contacts of the strand formed by residues 52 - 62 (chain K) in PDB entry 1I5L
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 GLU 52 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2C PRO 4.0 4.9 - - - +
3C PRO 3.9 12.2 - - - +
4C ARG* 2.7 32.9 + - - +
10D ASN* 4.1 9.2 - - - +
13D LEU* 4.2 10.2 - - + +
33D GLY* 4.4 1.4 - - - -
34D TYR* 2.7 70.3 + - - +
48K ILE* 3.4 3.4 - - - -
49K GLN 2.9 38.6 + - - +
50K ASN 3.7 1.0 + - - -
51K GLY* 1.3 74.0 - - - -
53K VAL* 1.3 57.5 + - - +
54K VAL* 3.3 12.8 + - + +
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Residues in contact with VAL 53 (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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4C ARG* 2.5 37.5 + - + +
46K GLU* 4.0 35.9 - - + +
47K GLU 3.6 4.7 - - - +
48K ILE* 4.6 9.2 - - + +
51K GLY 5.4 1.6 - - - +
52K GLU* 1.3 69.6 - - - +
54K VAL* 1.3 57.8 + - - +
55K ARG* 3.2 27.1 + - - +
56K LYS* 4.3 12.6 - - + -
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Residues in contact with VAL 54 (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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4C ARG* 3.8 2.7 - - - +
34D TYR* 5.0 1.6 - - - +
25K ARG* 3.7 16.4 - - - +
47K GLU* 2.8 49.3 + - + +
49K GLN* 3.5 35.0 - - + +
52K GLU* 3.8 21.5 - - + +
53K VAL* 1.3 70.1 - - - +
55K ARG* 1.3 68.5 + - - +
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Residues in contact with ARG 55 (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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18J ILE* 4.5 21.7 - - - +
20J ARG* 4.4 3.8 - - - +
26J GLU* 2.5 41.8 + - - -
50J ASN* 5.9 3.0 - - - +
69J PHE* 3.9 17.9 - - - -
25K ARG* 5.9 0.8 - - - +
46K GLU* 3.4 2.1 - - - -
47K GLU* 2.8 53.7 + - + +
53K VAL* 3.2 10.7 + - - +
54K VAL* 1.3 90.2 + - - +
56K LYS* 1.3 78.5 + - - +
57K VAL* 4.3 10.8 - - + +
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Residues in contact with LYS 56 (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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45K ALA 3.5 6.1 - - - +
46K GLU* 2.6 40.8 + - + +
53K VAL* 4.3 10.3 - - + -
55K ARG* 1.3 83.6 - - - +
57K VAL* 1.3 73.9 + - - +
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Residues in contact with VAL 57 (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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69J PHE* 5.6 4.0 - - + -
71J SER* 3.5 26.2 - - - +
72J PRO 5.7 0.2 - - - +
27K PHE* 4.6 7.6 - - + -
44K ASP* 3.5 2.1 - - - -
45K ALA* 3.0 36.4 + - + +
46K GLU 5.9 0.2 - - - -
55K ARG* 4.3 17.0 - - + +
56K LYS* 1.3 86.9 - - - +
58K GLY* 1.3 67.0 + - - +
59K SER 3.9 2.7 - - - +
60K VAL* 3.2 31.6 - - + -
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Residues in contact with GLY 58 (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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71J SER* 5.2 0.4 + - - -
72J PRO* 5.7 3.3 + - - +
43K LEU* 3.5 7.3 - - - +
44K ASP* 2.8 31.4 + - - +
57K VAL* 1.3 72.5 - - - +
59K SER* 1.3 63.8 + - - +
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Residues in contact with SER 59 (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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8J VAL* 5.4 8.0 - - - +
71J SER* 2.8 23.7 + - - -
72J PRO* 3.2 29.6 - - - +
41K VAL* 5.5 4.0 - - - -
42K LEU 3.1 15.0 - - - -
43K LEU* 3.6 15.0 - - - -
45K ALA 5.6 0.4 - - - +
57K VAL* 3.0 4.2 - - - -
58K GLY* 1.3 81.8 - - - +
60K VAL* 1.3 65.6 - - - +
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Residues in contact with VAL 60 (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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69J PHE* 4.4 11.0 - - + -
70J VAL 3.7 7.4 - - - +
71J SER* 3.5 16.4 - - - -
72J PRO* 4.9 0.7 - - - -
27K PHE* 4.0 28.3 - - + -
41K VAL* 3.3 7.3 - - - +
42K LEU* 3.2 44.9 + - + +
45K ALA* 4.9 1.1 - - + -
57K VAL* 3.2 26.0 - - + -
59K SER* 1.3 86.1 - - - +
61K VAL* 1.3 67.1 + - - +
62K ILE* 4.1 13.0 + - + -
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Residues in contact with VAL 61 (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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5J PRO* 4.1 26.0 - - + +
8J VAL* 4.2 30.3 - - + -
9J LEU* 4.8 18.2 - - + -
38J MET* 4.9 16.1 - - + +
69J PHE* 3.2 6.6 - - - -
70J VAL* 3.2 38.9 + - + +
40K LEU 3.4 11.4 - - - +
41K VAL* 4.6 5.2 - - + -
60K VAL* 1.3 78.7 - - - +
62K ILE* 1.3 67.1 + - - +
63K ARG 4.0 0.5 + - - -
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Residues in contact with ILE 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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68J VAL* 3.7 7.6 - - + +
69J PHE* 4.5 9.0 - - + -
19K VAL* 4.5 13.2 - - + -
21K LEU* 4.4 4.3 - - + -
27K PHE* 4.1 33.9 - - + -
39K ASN* 3.2 5.9 - - - +
40K LEU* 3.1 35.5 + - + +
42K LEU* 4.3 20.0 - - + -
60K VAL* 4.4 12.6 - - + +
61K VAL* 1.3 78.1 - - - +
63K ARG* 1.3 78.3 + - - +
64K GLY* 3.1 3.5 + - - -
66K THR* 4.4 9.4 - - + -
67K VAL* 3.8 19.5 - - + -
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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