Contacts of the strand formed by residues 43 - 55 (chain A) in PDB entry 4IYT
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 LYS 43 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A VAL 4.8 3.3 - - - +
38A ASP 5.9 0.7 + - - -
41A TYR* 3.2 40.7 - - + +
42A ASN* 1.3 98.4 - - - +
44A ASP* 1.3 68.7 + - - +
45A ALA 3.7 1.2 + - - -
90A ASP* 4.5 6.3 + - - -
215A SER* 4.1 22.2 + - - -
216A HIS 3.7 10.8 - - - +
217A GLU* 3.1 36.6 + - - +
218A LYS* 3.7 13.3 + - - +
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Residues in contact with ASP 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL 5.1 2.0 - - - -
43A LYS* 1.3 75.9 - - - +
45A ALA* 1.3 58.2 + - - +
215A SER* 3.2 5.0 - - - -
216A HIS* 2.7 64.6 + - + +
218A LYS* 3.5 31.6 + - - +
219A GLY 4.8 0.7 + - - -
273A TRP* 3.5 39.7 - - + +
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Residues in contact with ALA 45 (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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35A PHE* 3.6 4.7 - - - +
36A VAL* 2.9 44.5 + - + +
41A TYR* 3.6 28.9 - - + +
43A LYS 3.7 1.2 + - - -
44A ASP* 1.3 77.2 - - - +
46A LEU* 1.3 62.7 + - - +
92A ILE* 5.6 0.2 - - + -
117A PHE* 4.4 13.7 - - + -
213A THR* 5.0 0.2 - - + -
214A VAL 3.2 10.3 - - - +
215A SER* 4.7 0.4 - - - -
273A TRP* 4.0 5.5 - - - -
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Residues in contact with LEU 46 (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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33A PHE* 3.7 17.3 - - + -
34A ASP 3.5 36.1 - - - +
35A PHE* 4.1 11.9 - - + +
45A ALA* 1.3 77.1 - - - +
47A ILE* 1.4 64.1 + - - +
48A LEU* 3.9 24.1 + - + +
212A ALA 3.9 0.7 - - - +
213A THR* 3.3 3.4 - - - -
214A VAL* 2.8 44.9 + - + +
226A PHE* 4.3 5.4 - - + -
271A VAL* 4.0 26.7 - - + -
273A TRP* 3.6 27.4 - - + -
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Residues in contact with ILE 47 (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 GLN 3.5 2.4 - - - +
34A ASP* 2.8 43.8 + - + +
36A VAL* 3.8 24.2 - - + -
46A LEU* 1.4 73.9 - - - +
48A LEU* 1.3 63.4 + - - +
49A LYS 4.2 0.4 + - - +
109A LEU* 3.9 22.9 - - + -
111A TYR* 5.0 4.5 - - + -
117A PHE* 4.0 20.6 - - + -
131A TYR* 3.9 26.5 - - + -
132A SER 6.1 0.2 - - - -
133A LYS* 4.3 23.1 - - + -
211A ILE* 4.2 11.7 - - + -
212A ALA 3.7 2.9 - - - -
213A THR* 3.8 14.6 - - - +
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ILE* 4.5 4.3 - - + -
32A GLN 3.3 5.6 - - - +
33A PHE* 3.6 31.2 - - + -
46A LEU* 4.0 24.5 - - + +
47A ILE* 1.3 73.5 - - - +
49A LYS* 1.3 59.9 + - - +
50A MET* 3.9 12.0 + - + +
82A LEU* 4.3 31.6 - - + -
210A PHE 3.8 0.3 - - - +
211A ILE* 3.3 5.9 - - - +
212A ALA 2.8 47.2 + - - +
214A VAL* 4.0 20.2 - - + -
226A PHE* 4.8 8.7 - - + -
228A ILE* 4.3 10.1 - - + -
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Residues in contact with LYS 49 (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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30A ASN 3.7 2.4 - - - +
31A ILE* 3.5 5.9 - - - +
32A GLN* 2.9 54.4 + - + +
47A ILE 4.1 1.0 - - - -
48A LEU* 1.3 71.9 - - - +
50A MET* 1.3 61.6 + - - +
51A GLN* 3.3 40.8 + - + +
133A LYS* 3.9 30.4 - - + +
134A THR 2.7 31.3 + - - +
135A ILE* 4.6 1.8 - - + +
209A SER* 4.0 4.5 - - - -
210A PHE 3.4 8.3 - - - +
211A ILE* 4.0 11.4 - - + -
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Residues in contact with MET 50 (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 ILE* 4.0 19.3 - - + -
48A LEU* 4.1 7.4 - - + +
49A LYS* 1.3 72.0 - - - +
51A GLN* 1.3 59.3 + - - +
80A ILE* 4.6 12.8 - - + -
81A GLY 4.9 0.7 - - - +
82A LEU* 4.2 20.6 - - + -
156A TRP* 4.2 13.7 - - + -
208A PRO* 3.5 4.7 - - - +
209A SER* 3.4 4.7 + - - -
210A PHE* 2.7 46.3 + - + +
211A ILE 4.0 2.7 - - - -
212A ALA* 3.8 37.7 - - + +
228A ILE* 4.1 26.9 - - + -
230A TYR* 3.2 19.8 + - + +
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Residues in contact with GLN 51 (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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30A ASN* 2.9 35.2 + - + +
32A GLN* 3.8 16.1 - - - +
49A LYS* 3.3 35.4 + - + +
50A MET* 1.3 79.7 - - - +
52A GLY* 1.3 60.7 + - - +
136A SER 4.8 1.9 - - - +
208A PRO* 3.2 14.1 - - - +
209A SER* 2.9 24.3 + - - +
230A TYR* 2.6 26.9 + - - -
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Residues in contact with GLY 52 (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 THR* 3.2 8.1 - - - -
30A ASN* 3.4 22.6 + - - -
51A GLN* 1.3 82.4 - - - +
53A PHE* 1.3 63.8 + - - +
207A ASN* 3.5 15.6 - - - +
208A PRO* 3.4 16.2 + - - +
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Residues in contact with PHE 53 (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 GLY 4.8 2.5 - - - -
27A VAL* 3.4 4.3 - - - +
28A THR* 2.8 43.1 + - - +
52A GLY* 1.3 74.1 - - - +
54A ILE* 1.3 64.5 + - - +
55A ASN* 3.6 31.4 - - + -
204A SER* 3.5 27.6 - - - -
205A GLY* 3.9 7.4 - - - -
206A PHE 3.3 26.7 - - - -
207A ASN* 3.5 24.5 - - - +
208A PRO* 3.9 1.9 - - - +
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Residues in contact with ILE 54 (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 GLY 3.7 2.2 - - - -
27A VAL* 4.1 8.7 - - + -
53A PHE* 1.3 78.7 - - - +
55A ASN* 1.3 68.0 + - - +
78A TYR* 3.7 27.3 - - + -
79A ASN 4.0 2.0 - - - +
80A ILE* 3.5 32.3 - - + -
205A GLY* 3.2 1.2 - - - -
206A PHE* 2.8 44.2 + - + +
208A PRO* 4.4 2.2 - - + -
230A TYR* 3.7 26.0 - - + -
231A GLY 3.8 16.6 - - - +
232A ARG* 3.4 29.8 - - + +
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Residues in contact with ASN 55 (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 GLY* 2.9 24.4 + - - +
53A PHE* 3.6 24.0 - - + -
54A ILE* 1.3 72.7 - - - +
56A SER* 1.3 64.1 + - - +
57A LYS* 2.9 45.0 + - + +
204A SER 3.7 6.7 + - - +
232A ARG* 2.8 26.9 + - - -
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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