Contacts of the strand formed by residues 61 - 69 (chain B) in PDB entry 4PC0
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 PHE 61 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B ARG* 4.7 2.9 - - - +
56B PRO* 3.9 21.5 - - + +
59B LYS* 3.3 42.2 + - + +
60B ASP* 1.3 96.1 - - - +
62B SER* 1.3 68.6 + - - +
63B ILE* 3.8 20.4 - - + -
85B GLN* 3.6 46.4 - - + +
86B LEU 3.2 17.3 - - - +
87B PRO* 4.6 2.2 - - + -
88B ASN* 3.7 10.4 + - - +
108B PHE* 5.0 5.8 - - + -
114B LYS* 6.1 1.6 - - - -
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Residues in contact with SER 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B VAL* 4.1 2.2 - - - -
54B THR 3.5 13.5 - - - -
55B ARG* 3.8 27.3 + - - +
56B PRO* 4.7 0.2 - - - -
61B PHE* 1.3 75.6 - - - +
63B ILE* 1.3 64.2 + - - +
64B HIS* 2.8 27.5 + - - -
85B GLN* 3.2 4.7 - - - -
86B LEU* 2.8 40.1 + - - +
87B PRO 5.6 0.2 - - - -
88B ASN* 3.9 6.0 + - - -
386B GLU* 5.0 5.2 + - - -
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASP* 4.4 2.1 - - - +
53B VAL* 3.6 5.9 - - - +
54B THR* 3.0 46.6 + - - +
56B PRO* 4.6 10.8 - - + -
61B PHE* 3.8 26.5 - - + -
62B SER* 1.3 74.8 - - - +
64B HIS* 1.3 73.1 + - - +
65B ARG* 4.9 7.9 - - + +
83B SER* 4.1 18.2 - - - -
84B VAL 3.6 4.5 - - - +
85B GLN* 4.3 12.1 - - + +
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Residues in contact with HIS 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B TRP* 3.6 22.7 - - + -
50B LEU 6.1 0.2 - - - +
52B ASP 4.4 6.5 + - - +
53B VAL* 3.4 21.9 - - + +
55B ARG* 5.6 1.8 - - - -
62B SER* 2.8 32.6 + - - -
63B ILE* 1.3 80.2 - - - +
65B ARG* 1.3 63.2 + - - +
83B SER* 3.3 4.9 - - - -
84B VAL 2.7 35.8 + - - +
86B LEU* 3.4 31.0 - - + +
383B ASN* 3.5 18.6 + - - -
385B ASN* 4.1 11.5 + - + +
386B GLU* 3.9 16.7 - - + +
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Residues in contact with ARG 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B TRP* 3.4 9.4 - - - -
50B LEU* 2.8 59.2 + - + +
52B ASP* 3.1 43.5 + - - +
54B THR* 6.5 0.2 - - - -
63B ILE* 4.9 7.9 - - + -
64B HIS* 1.3 83.8 - - - +
66B LEU* 1.3 59.3 + - - +
81B ILE* 3.9 17.8 - - + +
82B ALA 3.2 11.7 - - - +
83B SER* 4.4 8.7 - - - -
84B VAL 4.9 0.2 - - - +
118B GLU* 5.5 6.4 - - + +
119B ILE* 4.7 5.1 - - - +
154B TYR* 2.9 41.4 + - - -
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA* 5.1 0.9 - - + -
48B GLN 3.5 9.0 - - - +
49B TRP* 3.5 52.0 - - + +
50B LEU* 4.5 2.0 - - - -
65B ARG* 1.3 73.3 - - - +
67B VAL* 1.3 60.6 + - - +
68B LEU* 3.8 17.2 + - + -
81B ILE* 3.4 8.3 - - - +
82B ALA* 2.9 33.9 + - + +
84B VAL* 3.8 24.5 - - + -
381B SER* 5.1 0.2 - - - -
391B CYS* 3.6 31.2 - - + -
399B MET* 4.0 17.3 - - + -
401B VAL* 4.9 1.1 - - + -
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B THR* 4.0 2.1 + - - +
47B ALA* 3.6 7.4 + - - -
48B GLN* 2.7 48.5 + - + +
50B LEU* 3.7 35.0 - - + -
66B LEU* 1.3 73.1 - - - +
68B LEU* 1.3 62.6 + - - +
79B LEU* 4.1 13.0 - - + -
80B VAL 3.7 4.7 - - - +
81B ILE* 4.9 2.5 - - + +
130B ALA* 3.7 32.2 - - + +
131B ARG 5.1 0.2 - - - +
132B TYR* 4.9 2.2 - - + -
140B ILE* 4.1 24.2 - - + -
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 4.5 15.7 - - + -
44B SER* 4.1 7.2 - - - +
46B THR* 3.5 25.1 - - - +
47B ALA* 4.2 11.9 - - + -
66B LEU* 4.1 13.5 - - + +
67B VAL* 1.3 80.1 - - - +
69B GLY* 1.3 62.1 + - - +
79B LEU* 3.5 11.2 - - - +
80B VAL* 2.8 45.1 + - + +
82B ALA* 3.8 27.8 - - + -
117B ILE* 5.3 0.2 - - + -
393B VAL* 4.4 6.1 - - + -
399B MET* 3.9 30.3 - - + -
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Residues in contact with GLY 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LEU* 5.4 0.9 - - - +
42B TRP 4.9 1.6 - - - +
43B PRO 3.7 0.9 - - - +
44B SER* 3.0 32.3 + - - -
45B LEU 5.1 0.9 - - - -
46B THR* 3.7 4.3 - - - +
68B LEU* 1.3 76.4 - - - +
70B THR* 1.3 66.8 + - - +
78B HIS 3.6 9.9 - - - -
80B VAL* 4.4 2.8 - - - +
127B VAL* 3.9 19.3 - - - -
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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
------------------------------------------------------------
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