Contacts of the strand formed by residues 58 - 66 (chain A) in PDB entry 5EWL
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 ILE 58 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LYS* 3.4 16.6 - - + +
27A VAL* 4.3 8.3 - - + -
54A PHE 5.2 1.0 + - - -
55A THR* 3.3 24.0 - - - +
57A LYS* 1.3 100.3 - - + +
59A GLN* 1.3 59.4 + - - +
60A LEU* 4.4 7.4 - - + -
313A ILE* 3.3 34.1 - - + -
314A HIS* 3.4 39.5 + - + +
317A PHE* 3.7 38.8 - - + -
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Residues in contact with GLN 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PRO* 3.9 28.2 - - + +
25A LYS 2.8 9.8 + - - +
26A ILE* 3.3 26.4 - - + +
27A VAL 3.0 23.1 + - - -
50A ASN* 3.5 27.2 - - + +
55A THR* 4.3 11.6 + - - -
58A ILE* 1.3 74.8 - - - +
60A LEU* 1.3 70.0 + - - +
61A GLN* 5.6 0.7 - - - +
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 5.0 0.2 - - - -
27A VAL* 3.2 15.5 - - + +
29A ILE* 3.5 31.0 - - + -
46A VAL* 3.6 19.4 - - + +
49A ALA* 4.3 10.5 - - + -
50A ASN* 2.8 39.7 + - - +
58A ILE* 4.4 3.4 - - + -
59A GLN* 1.3 81.2 - - - +
61A GLN* 1.3 62.0 + - - +
306A VAL* 5.5 0.7 - - + -
310A ALA* 3.7 32.3 - - + -
313A ILE* 3.9 27.1 - - + -
314A HIS* 4.9 9.9 - - + -
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Residues in contact with GLN 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 3.5 35.0 - - + +
27A VAL 3.1 5.9 + - - -
28A ASN* 3.2 29.1 + - - +
29A ILE* 2.9 24.8 + - - +
46A VAL* 4.3 2.7 - - - -
59A GLN* 5.6 0.7 - - - +
60A LEU* 1.3 75.5 - - - +
62A ALA* 1.3 72.3 + - - +
63A THR* 3.7 1.8 + - - +
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ILE 3.5 5.4 - - - -
42A PHE* 3.4 27.1 - - + -
43A ARG* 4.0 24.3 - - + +
46A VAL* 3.9 24.7 - - + +
61A GLN* 1.3 80.7 - - - +
63A THR* 1.3 59.0 + - - +
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Residues in contact with THR 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ASN* 3.4 30.0 + - - +
29A ILE 2.9 8.5 + - - +
30A GLY* 3.1 3.1 - - - -
31A ALA 3.0 21.5 + - - -
42A PHE* 3.3 1.6 - - - -
61A GLN* 4.8 1.2 + - - +
62A ALA* 1.3 72.3 + - - +
64A SER* 1.3 64.6 + - - +
81A ASP 3.4 26.2 - - - +
82A LEU* 3.8 8.7 - - + -
85A SER* 3.7 17.3 - - - +
87A VAL* 4.2 7.6 - - - -
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Residues in contact with SER 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA* 3.2 16.6 - - - -
33A LEU* 4.8 1.3 - - - -
39A GLU* 2.6 44.4 + - - +
42A PHE* 3.9 20.5 - - - -
43A ARG* 4.3 7.8 + - - -
62A ALA 4.4 0.4 - - - -
63A THR* 1.3 79.7 - - - +
65A VAL* 1.4 70.5 + - - +
82A LEU* 4.0 2.2 - - - -
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Residues in contact with VAL 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA 2.9 14.6 + - - +
32A VAL* 3.3 8.4 - - + -
33A LEU* 2.9 24.8 + - - +
39A GLU* 3.6 9.7 - - - +
64A SER* 1.4 77.5 - - - +
66A THR* 1.3 68.8 + - - +
68A ARG* 4.2 8.3 - - - +
74A MET* 4.0 14.6 - - + -
77A SER* 3.7 15.7 - - - +
81A ASP* 3.4 39.7 - - + +
82A LEU* 4.4 9.4 - - + -
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Residues in contact with THR 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A VAL* 4.3 3.8 - - - +
33A LEU 3.0 15.3 - - - +
34A SER 3.6 9.2 - - - +
35A THR* 3.6 33.2 - - - +
36A LYS* 4.2 1.6 - - - +
39A GLU* 3.9 14.5 + - + +
65A VAL* 1.3 82.0 - - - +
67A HIS* 1.3 68.0 + - - +
68A ARG* 3.3 33.3 + - - +
74A MET* 4.4 0.2 - - - +
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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