Contacts of the strand formed by residues 57 - 64 (chain L) in PDB entry 5GAG
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 VAL 57 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1952A A 3.9 33.0 - - - +
2561A U 4.5 20.2 - - - +
22L ILE* 4.9 6.3 - - + -
40L LYS* 4.2 25.8 - - + -
41L ILE 3.5 13.0 - - - +
42L THR* 4.9 1.8 - - - +
55L GLY 3.9 7.6 - - - +
56L ASP* 1.3 73.9 - - - +
58L LEU* 1.3 68.5 + - - +
89L ASN* 3.3 15.2 + - - +
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Residues in contact with LEU 58 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L LYS* 3.6 7.2 - - - +
41L ILE* 2.8 59.3 + - + +
43L ILE* 4.3 12.3 - - + -
52L VAL* 3.7 29.8 - - + -
56L ASP* 4.2 11.0 - - + +
57L VAL* 1.3 79.4 - - - +
59L LYS* 1.3 71.6 + - - +
86L LEU* 4.1 13.9 - - + -
87L LEU 4.0 10.1 - - - +
89L ASN* 4.1 16.6 - - + +
95L ILE* 4.0 10.5 - - + -
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Residues in contact with LYS 59 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2562A U 4.5 4.4 + - - -
25L LEU* 3.8 22.0 - - + +
38L ILE* 4.5 4.9 - - + -
39L ILE 3.3 10.1 - - - +
40L LYS* 3.5 36.1 - - + +
41L ILE* 5.0 0.2 - - - -
58L LEU* 1.3 83.0 - - - +
60L ALA* 1.3 64.4 + - - +
86L LEU* 3.8 1.9 - - - -
87L LEU* 2.9 32.0 + - + +
88L ASN 4.1 11.4 + - - +
89L ASN* 3.7 25.1 + - - +
90L ASN 5.6 0.4 + - - -
92L GLU* 2.9 32.2 + - + +
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Residues in contact with ALA 60 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L ASP 3.4 0.7 - - - +
38L ILE* 3.2 5.7 - - - +
39L ILE* 2.9 37.9 + - + +
41L ILE* 3.9 30.7 - - + -
59L LYS* 1.3 78.9 - - - +
61L VAL* 1.3 59.8 - - - +
84L CYS* 4.3 11.4 - - - -
85L VAL 3.4 15.7 - - - +
86L LEU* 4.3 2.2 - - + -
87L LEU* 3.8 9.2 - - - +
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Residues in contact with VAL 61 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L GLY 4.2 9.2 - - - +
37L ASP 3.2 8.5 - - - +
38L ILE* 4.6 0.2 - - - +
60L ALA* 1.3 72.9 - - - +
62L VAL* 1.3 64.9 + - - +
63L VAL* 3.4 13.3 + - + +
84L CYS* 3.1 4.0 - - - +
85L VAL* 2.9 42.9 + - + +
87L LEU* 3.9 14.8 - - + +
107L LEU* 4.0 19.7 - - + -
112L PHE* 4.3 21.5 - - + -
115L ILE* 3.6 28.5 - - + -
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Residues in contact with VAL 62 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2L ILE* 3.9 16.2 - - + -
8L LEU* 4.6 5.4 - - + -
33L ALA* 4.3 13.7 - - + -
34L GLY 3.6 14.8 - - - +
35L VAL* 3.2 6.1 - - - -
36L GLY* 2.8 28.2 + - - -
37L ASP 2.9 15.2 + - - +
39L ILE* 4.1 26.5 - - + -
61L VAL* 1.3 74.1 - - - +
63L VAL* 1.3 59.3 + - - +
64L ARG 4.0 7.4 - - - +
65L THR* 3.7 29.8 - - + -
83L ALA 4.0 3.1 - - - +
84L CYS* 3.9 6.1 - - + -
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Residues in contact with VAL 63 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11L ALA* 4.2 17.5 - - + -
35L VAL* 3.7 18.2 - - - +
61L VAL* 3.4 20.4 + - + +
62L VAL* 1.3 74.7 - - - +
64L ARG* 1.3 76.9 + - + +
79L PHE* 3.9 6.6 - - - -
83L ALA 3.0 21.9 + - - +
84L CYS* 4.0 2.9 - - - +
85L VAL* 3.9 18.4 - - + -
103L VAL* 4.0 22.1 - - + +
104L THR* 4.6 1.2 + - - -
107L LEU* 3.7 26.7 - - + -
115L ILE* 4.8 3.8 - - + -
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Residues in contact with ARG 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9L ASN* 5.6 2.8 - - - +
10L VAL 5.3 1.2 + - - -
11L ALA* 3.9 13.1 - - - +
35L VAL* 4.7 1.5 - - - +
62L VAL* 3.6 3.4 - - - +
63L VAL* 1.3 89.2 - - + +
65L THR* 1.3 66.7 + - - +
79L PHE* 3.3 23.8 - - + -
81L GLY 4.0 4.0 - - - +
82L ASN* 3.4 3.3 - - - +
83L ALA* 2.8 59.7 + - - +
99L ILE* 5.9 0.2 - - - +
100L PHE 3.0 28.5 + - - -
101L GLY* 3.2 12.0 + - - -
102L PRO* 2.9 28.2 + - - +
103L VAL* 4.9 0.6 - - - +
68Q GLU* 3.2 40.2 + - - +
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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