Contacts of the strand formed by residues 79 - 85 (chain A) in PDB entry 5UM9
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 79 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 3.5 31.2 - - + -
26A TYR* 3.8 27.1 - - + +
29A ARG* 3.6 4.9 - - + +
31A VAL* 3.8 25.6 - - + -
74A MET* 3.0 47.9 + - + +
75A MET* 3.6 10.8 + - - +
77A ASN* 3.9 10.5 - - + +
78A GLY* 1.3 77.3 - - - +
80A LYS* 1.3 64.1 - - - +
81A PRO* 3.2 11.4 - - - +
191A MET* 5.7 0.2 - - + -
194A LEU* 3.8 19.1 - - + -
196A ALA* 5.7 0.9 - - + -
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Residues in contact with LYS 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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28A GLY* 4.8 14.1 + - - +
29A ARG 2.9 15.1 + - - +
30A LYS* 3.2 34.6 - - + +
31A VAL 2.9 23.9 + - - -
75A MET* 4.3 4.5 - - - -
78A GLY 4.3 4.3 - - - +
79A ILE* 1.3 75.2 - - - +
81A PRO* 1.3 63.5 - - - +
298A TRP* 3.5 31.7 - - + +
335A SER* 2.8 40.8 + - - +
336A THR* 3.6 26.1 - - + +
337A LEU 5.1 1.0 - - - +
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Residues in contact with PRO 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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31A VAL* 3.3 7.9 - - + +
33A ILE* 3.4 33.0 - - + -
71A THR* 4.5 11.2 - - + -
74A MET* 4.2 17.5 - - + -
75A MET* 3.9 11.9 - - + -
79A ILE 3.2 11.9 - - - +
80A LYS* 1.3 84.4 - - - +
82A VAL* 1.3 60.1 + - - +
83A TYR* 4.4 14.4 - - + -
150A ILE* 3.7 6.4 - - + +
151A PRO* 3.7 7.3 - - - +
298A TRP* 2.9 27.1 + - + +
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Residues in contact with VAL 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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31A VAL 2.9 14.3 + - - +
32A ALA* 3.4 12.6 - - + -
33A ILE 2.9 22.4 + - - -
81A PRO* 1.3 75.2 - - - +
83A TYR* 1.3 71.5 + - - +
84A VAL* 3.6 3.6 + - + +
151A PRO* 3.4 25.1 - - + +
153A LEU* 4.1 16.2 - - + -
166A LEU* 4.7 3.8 - - + -
172A VAL* 3.9 19.3 - - + -
296A LEU* 4.0 28.0 - - + -
298A TRP* 4.7 2.2 - - + -
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Residues in contact with TYR 83 (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 ILE* 3.6 42.0 - - + +
35A ALA* 3.9 17.0 - - + -
38A SER* 4.6 7.0 - - - -
42A PHE* 6.1 0.2 - - - -
67A MET* 3.4 23.6 - - + -
70A ARG* 5.0 7.0 - - - +
71A THR* 2.7 32.8 + - - +
74A MET* 4.6 2.8 - - - -
81A PRO* 4.4 11.4 - - + -
82A VAL* 1.3 75.2 - - - +
84A VAL* 1.3 59.4 + - - +
85A PHE* 4.0 9.6 - - + -
145A LEU* 3.7 40.8 - - + -
150A ILE* 3.9 15.7 - - + -
151A PRO 3.2 6.1 + - - -
152A TYR* 3.1 6.9 - - + +
153A LEU 2.9 25.5 + - - +
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Residues in contact with VAL 84 (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 ALA* 4.3 0.9 - - + -
33A ILE 2.9 6.8 + - - +
34A ASP* 4.0 0.5 - - - +
35A ALA* 3.2 22.3 + - - -
82A VAL* 4.0 13.2 - - + +
83A TYR* 1.3 76.8 - - - +
85A PHE* 1.3 66.3 + - - +
153A LEU* 3.4 15.0 - - + +
155A ALA* 4.1 10.1 - - + +
159A ALA* 3.8 34.6 - - + +
162A SER* 4.1 8.3 - - - -
163A CYS* 3.7 25.4 - - - -
166A LEU* 4.0 23.6 - - + -
289A LEU* 4.9 0.9 - - + -
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Residues in contact with PHE 85 (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 ALA* 3.7 21.8 - - + -
36A SER* 5.0 2.5 - - - -
39A ILE* 4.3 8.1 - - + -
67A MET* 5.4 1.3 - - + -
83A TYR* 4.0 11.4 - - + -
84A VAL* 1.3 76.6 - - - +
86A ASN* 1.3 63.7 + - - +
138A ASN* 3.5 39.9 - - - +
141A CYS* 4.3 8.7 - - + -
142A LYS* 3.9 32.3 - - + +
145A LEU* 4.1 13.5 - - + -
152A TYR* 3.7 26.5 - + + -
153A LEU 2.9 17.0 + - - +
154A ASP* 4.1 12.8 - - - +
155A ALA* 3.0 31.9 + - - +
159A ALA* 4.0 2.2 - - - -
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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