Contacts of the strand formed by residues 55 - 62 (chain B) in PDB entry 5ITX
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 GLU 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LEU* 3.7 5.0 - - - +
51B ALA* 3.5 4.2 - - - +
52B ARG* 2.9 35.1 + - - +
53B GLY 3.4 0.9 + - - +
54B LYS* 1.3 85.0 - - - +
56B LEU* 1.3 60.9 + - - +
76B VAL* 3.4 17.9 - - + +
77B PHE 3.4 7.0 - - - +
78B ARG* 3.2 33.0 + - + -
128B LYS 4.9 0.3 - - - +
129B TRP* 3.5 21.7 - - + +
130B GLN* 2.9 39.7 + - - +
133B ARG* 3.5 21.2 - - - +
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Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.8 19.1 - - + +
10B ALA* 4.0 13.5 - - + +
11B SER* 3.7 31.4 - - - +
14B VAL* 5.3 0.9 - - + -
49B ALA* 4.6 3.1 - - + -
50B SER 3.5 13.2 - - - +
51B ALA* 4.8 1.3 - - - -
55B GLU* 1.3 76.1 - - - +
57B ARG* 1.3 73.8 + - - +
58B LEU* 4.1 21.1 - - + +
75B LEU 3.8 0.2 - - - +
76B VAL* 3.2 1.9 - - - -
77B PHE* 2.7 47.4 + - + +
79B PHE* 4.1 10.5 - - + -
85B PHE* 4.1 15.5 - - + -
129B TRP* 4.0 3.4 - - - -
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Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B ALA* 3.4 3.3 - - - +
50B SER* 2.8 42.8 + - - +
56B LEU* 1.3 76.8 - - - +
58B LEU* 1.3 70.0 + - - +
59B ILE* 4.3 16.9 - - + +
74B ALA* 4.1 8.1 - - + -
75B LEU 3.2 9.4 - - - +
76B VAL* 4.2 2.9 - - + +
127B GLY* 2.9 41.3 + - - -
128B LYS* 4.4 0.6 - - - +
129B TRP* 3.4 62.2 - - + +
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Residues in contact with LEU 58 (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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14B VAL* 3.8 29.8 - - + -
47B ILE* 3.9 17.5 - - + -
48B SER 3.3 5.4 - - - +
49B ALA* 4.0 7.6 - - + -
56B LEU* 4.1 11.6 - - + +
57B ARG* 1.3 74.1 - - - +
59B ILE* 1.3 62.9 + - - +
60B LEU* 4.5 5.1 - - + +
73B LEU 3.8 0.7 - - - +
74B ALA* 3.2 4.9 - - - +
75B LEU* 2.9 38.4 + - + +
77B PHE* 3.7 24.5 - - + -
85B PHE* 4.5 10.1 - - + -
101B PHE* 3.5 38.4 - - + -
112B LEU* 5.0 0.9 - - + -
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Residues in contact with ILE 59 (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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46B ARG 3.4 2.3 - - - +
47B ILE* 3.3 6.2 - - - -
48B SER* 2.8 45.0 + - - +
49B ALA* 6.0 0.4 - - - -
57B ARG* 4.3 24.9 - - + +
58B LEU* 1.3 78.6 - - - +
60B LEU* 1.3 66.0 + - - +
61B SER* 3.6 17.7 + - - +
72B PRO* 4.3 12.3 - - + -
73B LEU 3.4 10.1 - - - +
74B ALA* 4.6 6.5 - - + -
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Residues in contact with LEU 60 (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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27B VAL* 4.7 3.1 - - + -
38B VAL* 4.8 0.7 - - + -
40B PHE* 3.9 24.7 - - + -
45B TYR* 3.8 24.9 - - + -
46B ARG 3.4 3.8 - - - -
47B ILE* 3.9 19.1 - - + -
58B LEU* 4.5 7.9 - - + +
59B ILE* 1.3 77.1 - - - +
61B SER* 1.3 57.9 + - - +
62B PRO* 3.8 3.0 - - - +
72B PRO* 3.2 2.6 - - - +
73B LEU* 2.6 66.4 + - + +
75B LEU* 4.5 11.9 - - + -
101B PHE* 3.8 32.3 - - + -
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Residues in contact with SER 61 (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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45B TYR* 3.6 3.7 - - - +
46B ARG* 2.9 42.4 + - - +
48B SER* 5.4 1.4 + - - -
59B ILE* 3.6 19.2 + - - +
60B LEU* 1.3 73.1 - - - +
62B PRO* 1.3 72.1 - - - +
63B LEU* 3.5 1.7 + - - +
72B PRO* 3.9 12.3 - - - +
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Residues in contact with PRO 62 (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 PHE* 4.4 9.2 - - + -
42B SER* 3.5 19.1 - - - +
44B ALA 3.3 7.6 - - - +
45B TYR* 3.7 3.1 - - + -
60B LEU 3.8 2.9 - - - +
61B SER* 1.3 88.7 - - - +
63B LEU* 1.3 68.2 + - - +
64B PRO* 3.9 2.9 - - - +
66B ALA* 4.2 4.0 - - + +
68B PRO 5.8 0.4 - - - +
70B GLN* 3.4 39.3 - - + +
71B GLU 4.1 0.7 - - - +
72B PRO* 3.7 23.6 - - + -
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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