Contacts of the strand formed by residues 62 - 74 (chain L) in PDB entry 5G04
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 HIS 62 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34L SER* 3.6 8.5 - - - +
35L SER* 4.0 6.9 + - - -
54L TRP* 4.5 4.3 - - + -
56L SER* 2.9 42.2 + - - +
58L GLY 3.2 24.1 + - - -
59L SER 3.8 9.2 + - - -
60L GLN* 4.0 14.8 - - - +
61L PRO* 1.3 72.3 - - - +
63L LEU* 1.3 58.7 + - - +
139L ILE 3.5 1.0 - - - +
140L ALA* 3.5 1.2 - - - -
141L VAL* 2.9 47.6 + - + +
144L ASN* 4.8 1.1 + - - -
149L ARG 2.8 28.9 + - - -
151L THR* 3.3 21.2 + - - +
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Residues in contact with LEU 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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1600A ARG* 6.4 0.2 - - - +
33L LEU* 3.5 5.7 - - - -
34L SER* 3.0 41.1 + - - -
54L TRP* 3.7 5.7 - - - -
61L PRO* 3.1 27.1 - - + +
62L HIS* 1.3 78.1 - - - +
64L VAL* 1.4 66.3 + - - +
65L ASN* 3.5 19.7 - - - +
97L ARG* 4.6 4.5 - - - +
102L PHE* 6.2 0.2 - - + -
138L GLN* 3.1 34.3 - - - +
139L ILE 3.2 3.6 - - - -
140L ALA* 3.6 18.2 - - + -
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Residues in contact with VAL 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31L TRP* 3.6 36.6 - - + -
32L SER 3.4 5.2 - - - +
33L LEU* 3.8 11.4 - - + -
45L LEU* 5.1 0.2 - - + -
54L TRP* 3.6 26.2 - - + -
62L HIS 5.5 0.2 - - - +
63L LEU* 1.4 76.7 - - - +
65L ASN* 1.3 62.0 + - - +
66L ILE* 3.3 15.3 + - + +
137L ILE 3.6 4.5 - - - +
139L ILE* 2.9 43.4 + - + +
153L MET* 4.5 2.0 - - + -
156L ILE* 3.9 17.0 - - + -
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Residues in contact with ASN 65 (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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1600A ARG* 5.6 0.6 - - - +
30L VAL 3.2 3.5 - - - +
31L TRP* 3.7 1.0 - - - -
32L SER* 2.9 60.0 + - - +
34L SER* 4.4 4.5 + - - -
63L LEU* 3.5 25.3 - - - +
64L VAL* 1.3 68.8 - - - +
66L ILE* 1.3 59.3 + - - +
67L GLN* 4.0 2.0 - - - +
102L PHE* 2.9 38.5 - - + -
136L MET* 3.7 6.9 - - + +
137L ILE 3.5 6.3 - - - -
138L GLN* 3.0 29.1 + - - -
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Residues in contact with ILE 66 (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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29L ALA* 3.5 27.6 - - + -
30L VAL 3.3 3.1 - - - +
31L TRP* 3.6 51.8 - - + +
64L VAL* 3.3 17.7 - - + +
65L ASN* 1.3 75.8 - - - +
67L GLN* 1.4 59.8 - - - +
68L PHE* 3.7 19.2 - - + -
136L MET* 3.2 4.1 - - - +
137L ILE* 2.7 48.0 + - + +
139L ILE* 3.8 18.8 - - + -
156L ILE* 5.1 0.4 - - + -
158L ILE* 4.8 10.3 - - + -
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Residues in contact with GLN 67 (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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1292A GLU* 4.7 3.8 - - - +
1359A ASN* 4.8 1.0 - - - +
1361A ASP* 3.8 39.5 - - - +
1362A VAL* 6.0 0.7 - - - +
1400A LYS* 4.8 3.6 - - - +
1601A TYR* 5.2 0.2 + - - -
28L GLN 4.8 0.2 - - - +
29L ALA* 3.2 4.5 - - - -
30L VAL* 3.0 51.4 + - + +
32L SER* 4.0 5.5 + - - -
65L ASN* 4.0 13.9 - - - +
66L ILE* 1.4 77.0 - - - +
68L PHE* 1.3 63.9 + - - +
69L ARG 4.0 0.7 + - - -
102L PHE* 3.4 38.2 - - + -
135L PHE* 3.5 5.2 - - + +
136L MET* 4.2 19.7 - - + +
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Residues in contact with PHE 68 (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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1361A ASP* 4.5 7.8 - - - +
25L ILE* 3.9 40.8 - - + -
28L GLN* 5.6 2.7 - - + -
29L ALA* 3.6 23.6 - - + +
66L ILE* 3.7 27.6 - - + -
67L GLN* 1.3 74.9 - - - +
69L ARG* 1.3 64.7 + - - +
70L ARG 3.1 22.4 + - - +
72L THR* 3.6 17.9 - - - +
74L VAL* 4.6 2.0 - - + -
134L THR 4.0 6.3 - - - -
135L PHE* 2.8 37.7 + - - +
137L ILE* 3.5 33.0 - - + -
158L ILE* 4.6 9.0 - - + -
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Residues in contact with ARG 69 (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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1330A VAL 5.2 4.0 - - - -
1331A GLY* 5.0 12.5 - - - -
1332A GLY 5.2 2.0 - - - +
1357A THR* 4.1 31.3 + - - -
1358A ILE 4.4 14.8 + - - +
1359A ASN* 5.3 2.5 - - + +
1360A VAL* 5.1 22.3 - - + +
1361A ASP* 5.1 6.7 - - - -
1398A PHE* 3.2 53.5 - - - +
618H ASP* 5.3 14.9 + - - +
28L GLN* 4.3 43.7 + - + +
67L GLN 4.0 1.4 + - - -
68L PHE* 1.3 71.8 - - - +
70L ARG* 1.3 63.3 + - - +
135L PHE* 4.8 1.4 - - - -
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Residues in contact with ARG 70 (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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1394A TYR* 4.2 15.8 + - - -
1397A ASP* 3.8 22.4 - - + -
1398A PHE* 3.6 58.3 - - + +
615H GLU* 4.6 20.0 + - - +
617H LEU* 6.0 1.8 - - - +
23L ARG* 5.4 4.0 - - - +
25L ILE* 5.7 0.4 - - - +
28L GLN* 4.8 20.3 + - - +
68L PHE* 3.1 14.2 - - - +
69L ARG* 1.3 83.0 - - - +
71L LYS* 1.3 64.0 + - - +
72L THR* 2.7 59.4 + - - +
135L PHE* 4.7 1.3 - - - -
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Residues in contact with LYS 71 (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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1397A ASP* 3.4 27.2 + - + +
1401A PRO* 5.4 3.1 - - - -
1455A GLU* 4.2 17.2 + - - +
1456A THR* 3.3 43.1 + - + +
1459A GLN* 5.0 4.0 + - - -
70L ARG* 1.3 76.5 + - - +
72L THR* 1.3 62.1 + - - +
73L THR* 3.8 0.7 + - - -
100L ASN* 4.8 6.0 + - - -
133L ARG* 3.4 39.8 + - + +
134L THR* 3.9 28.8 - - - +
135L PHE* 3.6 36.2 - - + +
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Residues in contact with THR 72 (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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23L ARG* 5.9 0.7 - - - +
25L ILE* 4.0 32.1 - - + +
68L PHE* 3.6 23.5 - - - +
70L ARG* 2.7 43.9 + - - +
71L LYS* 1.3 72.0 - - - +
73L THR* 1.3 75.2 + - - +
74L VAL* 3.6 8.0 + - - +
133L ARG* 4.5 0.2 - - - -
134L THR 3.3 24.9 + - - +
160L THR* 4.0 9.4 - - + +
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Residues in contact with THR 73 (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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71L LYS 3.8 1.5 + - - -
72L THR* 1.3 75.8 - - - +
74L VAL* 1.3 61.1 + - - +
131L PRO* 3.6 28.3 - - + +
132L THR 3.5 11.0 - - - +
133L ARG* 2.8 48.1 + - - +
160L THR* 2.8 30.1 + - - -
161L PRO* 3.2 12.1 - - + +
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Residues in contact with VAL 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25L ILE* 3.5 30.7 - - + -
68L PHE* 4.6 2.7 - - + -
72L THR 3.9 8.5 - - - +
73L THR* 1.3 73.5 - - - +
75L LYS* 1.3 63.4 + - - +
76L THR 4.8 0.2 - - - +
124L LEU* 3.5 31.3 - - + +
131L PRO* 3.6 11.6 - - - +
132L THR* 3.0 23.3 + - - +
134L THR* 4.1 5.8 - - + -
137L ILE* 3.7 28.0 - - + -
158L ILE* 3.9 16.6 - - + -
159L TYR 3.7 6.1 - - - +
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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