Contacts of the strand formed by residues 40 - 49 (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 LEU 40 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5J PRO* 4.0 0.3 - - - +
9K LEU* 5.1 5.4 - - + -
19K VAL* 3.7 41.7 - - + -
31K LEU* 4.9 7.2 - - + -
33K GLY 3.5 4.7 - - - +
34K TYR* 4.1 14.1 - - + -
38K MET* 3.2 31.2 - - + +
39K ASN* 1.3 76.9 - - - +
41K VAL* 1.3 71.5 + - - +
42K LEU* 4.5 10.8 - - + -
60K VAL 4.5 0.2 - - - -
61K VAL* 3.4 6.6 - - - +
62K ILE* 3.1 37.3 + - + -
67K VAL* 4.2 11.9 - - + -
70K VAL* 3.9 18.6 - - + -
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Residues in contact with VAL 41 (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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3J PRO 4.7 1.1 - - - +
4J ARG 4.2 2.9 - - - -
5J PRO* 3.5 38.8 - - + -
8J VAL* 4.0 23.3 - - + -
32K ASP* 2.8 39.1 + - + +
33K GLY* 3.0 20.2 + - - +
40K LEU* 1.3 82.1 - - - +
42K LEU* 1.3 71.3 + - - +
43K LEU* 5.5 4.7 - - + -
59K SER* 5.5 1.8 - - - -
60K VAL 3.3 12.3 - - - +
61K VAL* 4.6 6.1 - - + -
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Residues in contact with LEU 42 (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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17K VAL* 4.1 13.7 - - + -
19K VAL* 3.9 18.8 - - + -
27K PHE* 3.8 31.2 - - + -
28K ARG 4.7 0.2 - - - +
29K GLY 4.3 11.2 - - - +
30K THR 3.2 4.7 - - - +
31K LEU* 3.9 23.8 - - + +
40K LEU* 4.5 4.0 - - + -
41K VAL* 1.3 85.4 - - - +
43K LEU* 1.3 65.0 + - - +
45K ALA* 4.1 20.4 - - + -
59K SER* 3.1 26.7 - - - -
60K VAL* 3.2 18.0 + - + -
62K ILE* 4.3 10.5 - - + -
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Residues in contact with LEU 43 (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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29K GLY* 3.7 0.9 - - - -
30K THR* 3.0 41.5 + - + +
32K ASP* 3.3 40.2 - - + +
41K VAL* 5.5 3.8 - - + -
42K LEU* 1.3 76.3 - - - +
44K ASP* 1.3 80.4 + - - +
45K ALA 3.2 3.2 + - - -
58K GLY 3.5 4.7 - - - +
59K SER* 3.6 24.7 - - - -
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Residues in contact with ASP 44 (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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28K ARG 4.0 3.5 - - - +
29K GLY* 4.1 3.3 - - - -
30K THR* 5.4 2.4 + - - +
43K LEU* 1.3 80.4 - - - +
45K ALA* 1.3 58.1 + - - +
46K GLU* 5.2 2.6 - - - +
57K VAL 3.5 9.0 - - - -
58K GLY* 2.8 26.1 + - - +
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Residues in contact with ALA 45 (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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27K PHE* 4.2 11.2 - - + -
28K ARG 2.9 22.9 - - - +
29K GLY* 3.7 7.2 - - - -
42K LEU* 4.1 24.0 - - + +
43K LEU 3.3 0.4 - - - -
44K ASP* 1.3 76.2 - - - +
46K GLU* 1.3 61.6 + - - +
56K LYS* 3.5 2.8 - - - +
57K VAL* 3.0 41.2 + - + +
59K SER 5.2 0.2 - - - +
60K VAL* 4.9 1.3 - - + -
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Residues in contact with GLU 46 (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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27K PHE* 3.3 10.6 - - - -
28K ARG* 3.0 50.3 + - + +
44K ASP 5.2 2.0 - - - +
45K ALA* 1.3 79.0 - - - +
47K GLU* 1.3 60.7 + - - +
48K ILE* 3.9 7.9 + - + +
53K VAL* 4.0 30.8 - - + +
55K ARG 3.4 5.6 - - - +
56K LYS* 2.6 37.4 + - + +
57K VAL* 5.9 0.2 - - - -
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Residues in contact with GLU 47 (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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20J ARG* 4.0 15.9 + - - -
69J PHE* 4.2 6.1 - - - -
21K LEU* 5.7 0.7 - - - +
25K ARG* 3.4 34.0 + - + +
26K GLU 3.7 4.7 - - - +
27K PHE* 4.2 31.1 - - + -
46K GLU* 1.3 71.0 - - - +
48K ILE* 1.3 58.4 + - - +
53K VAL* 3.6 2.3 - - - -
54K VAL* 2.8 56.1 + - + +
55K ARG* 2.8 45.0 + - + +
57K VAL* 6.1 0.2 - - - +
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Residues in contact with ILE 48 (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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24K GLY 4.6 0.2 - - - +
25K ARG* 3.7 6.1 - - - -
26K GLU* 2.7 55.3 + - + +
27K PHE 5.6 0.4 - - - -
28K ARG* 3.5 46.4 - - + +
46K GLU* 4.5 12.1 - - + +
47K GLU* 1.3 74.8 - - - +
49K GLN* 1.3 63.7 + - - +
50K ASN 4.3 0.7 + - - +
51K GLY* 3.8 26.9 - - - +
52K GLU 3.4 10.8 - - - +
53K VAL* 4.6 13.7 - - + -
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Residues in contact with GLN 49 (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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6D LEU 5.6 0.2 - - - -
7D ASP* 4.6 19.1 + - - +
10D ASN* 3.1 44.4 + - - +
34D TYR* 4.2 3.4 + - - -
24K GLY 5.2 1.8 - - - +
25K ARG* 3.0 48.3 + - - +
47K GLU 4.1 0.4 + - - -
48K ILE* 1.3 73.4 - - - +
50K ASN* 1.3 60.1 + - + +
51K GLY 2.6 15.0 + - - -
52K GLU 2.9 17.5 + - - +
54K VAL* 3.5 22.4 - - + +
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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