Contacts of the strand formed by residues 42 - 53 (chain C) in PDB entry 6A5T
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 THR 42 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40C VAL 3.4 2.4 + - - +
41C PRO* 1.3 80.7 - - - +
43C LEU* 1.3 65.3 + - - +
44C ALA* 5.1 0.3 - - - +
73C SER* 4.4 7.6 - - - -
76C VAL* 3.8 10.1 - - - -
161C LYS* 3.2 7.8 - - - +
162C GLY 3.0 16.8 + - - -
169C LYS 4.2 2.6 + - - -
170C TRP* 3.0 41.1 - - - +
172C PRO* 3.6 34.1 - - + -
237C SER* 4.8 7.0 - - - +
238C LEU* 4.2 15.7 - - + -
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Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C THR* 1.3 81.6 + - - +
44C ALA* 1.3 63.7 + - - +
71C LEU* 3.3 25.3 + - + +
73C SER* 3.6 15.4 + - - +
76C VAL* 3.6 12.6 - - + -
79C MET* 3.8 34.1 - - + -
96C VAL* 4.7 5.4 - - + -
129C VAL* 4.0 28.7 - - + -
130C GLY* 4.1 15.0 - - - +
159C ALA* 4.3 8.3 - - + +
160C LYS* 3.2 26.9 - - - +
161C LYS* 3.7 9.2 - - + +
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Residues in contact with ALA 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C THR* 5.1 0.9 - - - +
43C LEU* 1.3 76.3 - - - +
45C ILE* 1.3 65.5 + - - +
46C ASP* 3.4 2.4 + - - +
67C GLY 4.3 12.8 - - - +
68C LEU 5.2 0.4 - - - +
69C ILE 4.6 10.8 - - - +
71C LEU* 3.7 6.7 - - - -
159C ALA* 4.0 5.4 - - - -
160C LYS 2.9 30.7 + - - +
169C LYS* 4.3 19.1 - - + +
170C TRP* 3.8 19.0 + - + +
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Residues in contact with ILE 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ALA* 1.3 74.5 - - - +
46C ASP* 1.3 60.8 + - - +
47C LEU 4.6 2.0 - - - +
48C VAL* 4.1 22.7 - - + -
66C LEU* 3.0 49.5 + - + +
67C GLY* 3.6 15.2 + - - +
69C ILE* 4.7 8.6 + - + +
71C LEU* 4.3 12.0 - - + +
98C LEU* 5.0 12.8 - - + -
118C LEU* 5.1 3.4 - - + -
157C CYS* 4.2 20.0 - - + -
158C ILE 3.4 15.3 - - - +
159C ALA* 4.7 3.4 - - + -
169C LYS* 3.4 20.3 + - - -
170C TRP* 5.6 0.2 - - - -
71L ALA* 4.3 2.5 - - + +
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Residues in contact with ASP 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ALA 3.4 7.1 + - - +
45C ILE* 1.3 75.5 - - - +
47C LEU* 1.3 79.2 + - + +
48C VAL 4.0 1.3 - - - -
158C ILE 3.2 6.2 + - - +
160C LYS* 3.6 40.9 + - + +
166C GLU* 4.0 7.0 - - - +
169C LYS* 4.5 5.9 + - - +
170C TRP* 3.8 22.6 - - + -
70L ASP* 3.8 20.2 - - - +
71L ALA* 5.1 0.4 - - - -
72L ARG* 4.3 9.2 + - - -
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ILE* 5.1 0.4 - - - -
46C ASP* 1.3 97.8 - - - +
48C VAL* 1.3 67.9 + - - +
49C GLU* 3.5 16.0 + - + +
89C ASP* 4.5 12.6 - - - +
90C TYR* 4.9 6.3 - - + -
156C ARG 4.8 0.2 - - - -
157C CYS* 3.9 0.9 - - - -
158C ILE* 3.3 41.2 + - + +
160C LYS* 3.9 21.8 - - - +
68L GLN* 5.6 9.9 - - + +
69L PHE 3.3 19.1 - - - +
70L ASP* 3.9 7.9 - - - +
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Residues in contact with VAL 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ILE* 4.1 17.7 - - + +
46C ASP 4.0 1.2 - - - -
47C LEU* 1.3 75.6 - - - +
49C GLU* 1.3 66.9 + - - +
50C ILE* 3.9 24.0 - - + +
62C ILE* 6.4 0.7 - - + -
63C SER* 3.2 51.6 - - - +
66C LEU* 4.4 7.4 - - + -
155C ILE* 5.2 5.6 - - + -
156C ARG 3.7 7.6 - - - +
157C CYS* 4.4 12.3 - - - +
68L GLN* 3.5 0.5 - - - +
69L PHE* 3.2 31.8 + - + -
70L ASP 5.2 0.2 - - - +
71L ALA* 4.6 3.5 - - + +
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Residues in contact with GLU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C LEU* 4.1 15.3 - - + +
48C VAL* 1.3 78.7 - - - +
50C ILE* 1.3 68.9 + - - +
51C LYS* 3.4 7.4 + - - +
90C TYR* 3.3 34.3 + - - -
156C ARG* 3.0 45.0 + - + +
158C ILE* 5.4 1.5 - - - +
66L MET* 4.2 22.6 - - + +
67L ILE 3.3 7.2 - - - +
68L GLN* 2.8 40.5 + - + -
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Residues in contact with ILE 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C VAL* 3.9 15.0 - - + +
49C GLU* 1.3 73.0 - - - +
51C LYS* 1.3 61.4 + - - +
52C MET 3.5 22.7 - - - +
53C ASN* 4.2 6.5 - - + +
59C ASP* 3.4 47.8 - - + +
62C ILE* 5.8 4.0 - - + -
63C SER 5.7 0.7 - - - +
153C LEU* 5.8 1.1 - - + -
154C ASN 4.3 3.6 - - - +
155C ILE* 3.8 21.5 - - + -
62L ARG* 3.9 21.9 + - - +
65L ARG 5.1 0.2 - - - +
66L MET* 3.9 5.4 - - - +
67L ILE* 3.2 30.2 + - + +
69L PHE* 4.1 11.6 - - + -
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Residues in contact with LYS 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C GLU 3.4 7.5 + - - +
50C ILE* 1.3 80.3 - - - +
52C MET* 1.3 67.6 + - + +
99C GLU* 4.3 14.4 + - - +
154C ASN* 3.3 26.5 + - - +
155C ILE 5.4 0.7 - - - +
156C ARG* 4.7 25.2 - - + +
62L ARG* 4.7 11.9 + - - -
65L ARG 4.8 8.6 - - - +
66L MET* 4.2 28.0 - - + -
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Residues in contact with MET 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ILE* 3.5 4.8 - - - +
51C LYS* 1.3 85.1 - - + +
53C ASN* 1.3 65.1 + - - +
54C THR* 4.5 13.5 - - + -
152C GLU* 3.2 39.9 - - + +
153C LEU* 3.6 5.3 - - - +
154C ASN* 2.9 50.1 + - + +
62L ARG* 4.6 7.4 - - - +
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Residues in contact with ASN 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C ILE* 4.2 9.4 - - + +
52C MET* 1.3 76.5 - - - +
54C THR* 1.3 73.6 + - - +
55C SER* 2.3 53.4 + - - -
57C LEU 3.2 12.1 + - - -
58C ALA 4.0 3.2 + - - -
59C ASP* 2.8 29.5 + - - +
62C ILE* 5.4 3.0 - - - +
152C GLU 3.9 2.3 - - - +
153C LEU* 4.6 11.4 - - + +
62L ARG* 3.7 21.9 + - - +
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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