Contacts of the strand formed by residues 74 - 82 (chain A) in PDB entry 4CYM
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 74 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ARG 3.3 4.8 + - - +
23A GLU* 3.2 47.4 - - + +
24A HIS* 2.9 25.5 + - - -
66A VAL* 4.0 22.4 - - + -
67A LEU 3.2 10.5 - - - +
68A ASN* 3.7 21.8 - - - +
69A TRP 4.3 0.7 - - - +
73A THR* 1.3 77.2 - - - +
75A VAL* 1.3 68.4 + - - +
76A ARG* 3.6 17.3 - - + +
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Residues in contact with VAL 75 (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 HIS* 3.6 15.5 - - + +
26A PHE* 4.3 20.2 - - + -
65A LYS 3.5 4.0 - - - +
66A VAL* 3.5 0.6 - - - -
67A LEU* 2.9 59.0 + - + +
69A TRP* 4.1 25.6 - - + -
73A THR* 5.6 0.9 - - - +
74A LEU* 1.3 79.3 - - - +
76A ARG* 1.3 61.7 + - - +
77A LEU* 4.1 23.6 - - + -
189A VAL* 4.5 13.2 - - + -
193A LEU* 4.7 4.3 - - + -
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Residues in contact with ARG 76 (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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23A GLU* 3.0 31.8 + - - +
24A HIS 2.6 17.6 + - - +
25A LEU* 3.4 28.9 - - + +
26A PHE* 2.9 27.4 + - - +
64A LEU* 4.2 17.8 - - + +
65A LYS 3.5 4.0 - - - -
66A VAL* 4.5 27.6 - - + +
74A LEU* 3.6 15.5 - - + +
75A VAL* 1.3 73.3 - - - +
77A LEU* 1.3 63.2 + - - +
78A GLN 4.0 0.4 - - - -
554D GLU* 5.0 8.1 - - - -
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Residues in contact with LEU 77 (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 PHE* 3.8 33.2 - - + -
28A VAL* 4.1 17.9 - - + -
45A TYR* 4.4 26.9 - - + +
63A ALA 3.5 0.3 - - - +
64A LEU* 3.3 8.6 - - - +
65A LYS* 2.6 51.6 + - + +
67A LEU* 4.5 5.2 - - + -
75A VAL* 4.1 8.3 - - + -
76A ARG* 1.3 72.9 - - - +
78A GLN* 1.3 63.2 + - - +
79A LEU* 3.5 14.8 + - + +
103A PHE* 6.2 2.7 - - + -
185A ALA* 5.4 2.9 - - + -
189A VAL* 4.1 23.3 - - + -
192A ILE* 5.7 0.2 - - + -
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Residues in contact with GLN 78 (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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25A LEU* 3.9 33.0 - - + +
26A PHE 2.8 14.8 + - - +
27A LYS* 4.1 8.4 - - - +
28A VAL* 2.8 28.4 + - - +
63A ALA 3.8 3.4 - - - -
64A LEU* 4.6 7.0 - - + -
76A ARG 4.0 0.6 + - - -
77A LEU* 1.3 68.8 - - - +
79A LEU* 1.3 61.1 + - - +
80A TRP* 3.4 20.2 - - + +
549D VAL 4.6 1.7 - - - +
550D TYR* 3.1 53.6 + - + +
551D TYR 4.8 0.4 + - - -
553D VAL* 3.7 21.2 - - - +
554D GLU 4.7 1.6 + - - -
587D ASN* 5.5 2.6 + - - +
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Residues in contact with LEU 79 (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 VAL* 4.0 28.5 - - + +
30A VAL* 4.4 11.0 - - + -
42A ILE* 4.0 33.4 - - + +
45A TYR* 4.2 18.4 - - + -
46A VAL* 4.1 17.9 - - + -
62A PHE* 3.2 8.8 - - - +
63A ALA 2.7 45.4 + - - +
65A LYS* 4.6 6.1 - - + -
77A LEU* 4.3 18.8 - - + +
78A GLN* 1.3 71.9 - - - +
80A TRP* 1.3 60.7 + - - +
81A ASP* 3.5 2.8 + - - +
103A PHE* 4.8 9.9 - - + -
550D TYR* 5.3 0.8 - - - -
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Residues in contact with TRP 80 (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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27A LYS* 3.2 36.0 - - + +
28A VAL 2.9 14.1 + - - +
29A LEU* 3.8 12.1 - - + -
30A VAL* 3.0 25.3 + - - +
60A VAL* 4.4 7.9 - - + -
61A ASP 3.6 4.7 - - - -
62A PHE* 3.5 37.0 - + - -
78A GLN* 3.4 37.7 - - + +
79A LEU* 1.3 71.5 - - - +
81A ASP* 1.3 63.8 + - - +
82A ILE* 3.3 9.9 + - + +
94A VAL* 5.0 1.3 - - + -
95A TYR* 3.7 41.3 - + + -
513D LEU* 4.8 7.2 - - + -
550D TYR 3.7 18.4 + - - -
551D TYR* 4.1 30.3 - + - -
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Residues in contact with ASP 81 (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 VAL 4.1 2.7 - - - -
38A LYS* 3.8 17.0 - - - +
39A THR* 2.5 41.0 + - - +
42A ILE* 3.4 27.3 - - + +
57A THR* 4.3 3.1 + - - +
60A VAL* 3.5 4.9 - - - +
61A ASP* 2.7 60.1 + - + +
62A PHE* 5.2 1.3 - - - -
79A LEU 3.5 1.8 + - - +
80A TRP* 1.3 70.1 - - - +
82A ILE* 1.3 65.9 + - - +
83A ALA 4.0 0.2 + - - -
1199A MG 4.2 3.0 - - - -
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Residues in contact with ILE 82 (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 LEU* 3.8 27.8 - - + -
30A VAL 3.2 11.9 + - - +
31A ILE* 3.9 16.5 - - + -
32A GLY 4.6 0.3 + - - +
38A LYS* 2.9 28.4 - - - +
59A GLY 4.1 2.2 - - - +
60A VAL* 4.5 9.0 - - + -
80A TRP* 3.6 9.4 - - + +
81A ASP* 1.3 79.6 + - - +
83A ALA* 1.3 73.1 + - - +
84A GLY* 4.3 0.2 - - - -
86A GLU* 4.0 15.3 - - + -
92A THR* 5.3 2.0 - - + -
95A TYR* 3.9 27.4 - - + -
96A TYR* 3.9 12.8 - - + -
120A TRP* 4.5 14.8 - - + -
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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