Contacts of the strand formed by residues 74 - 80 (chain F) in PDB entry 5GJQ
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 ILE 74 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69F GLU* 3.7 0.9 - - - -
70F ILE* 2.7 53.0 + - + -
71F ASP* 2.9 20.8 + - + +
73F HIS* 1.3 114.0 - - + +
75F GLY* 1.3 62.2 + - - +
96F THR* 5.2 2.2 - - + -
107F MET 4.1 1.1 - - - +
109F VAL* 3.8 25.8 - - + -
112F VAL* 3.7 31.0 - - + -
143F PHE* 4.5 9.4 - - + -
144F GLY 3.5 9.0 - - - +
145F GLY* 4.2 6.3 - - - -
226F PHE* 4.6 2.7 - - - +
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Residues in contact with GLY 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F LEU* 4.1 6.5 - - - -
68F VAL 3.4 10.3 - - - -
70F ILE* 4.3 1.3 - - - -
74F ILE* 1.3 77.4 - - - +
76F CYS* 1.3 60.4 + - - +
143F PHE* 3.4 3.8 - - - -
144F GLY 2.8 36.3 + - - -
220F VAL* 4.6 0.2 - - - +
226F PHE* 3.6 23.0 - - - -
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Residues in contact with CYS 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F LEU* 4.2 3.3 - - - +
66F LYS 3.8 0.5 - - - +
67F ILE* 3.3 6.0 - - - +
68F VAL* 2.9 40.8 + - + +
70F ILE* 3.9 15.3 - - + -
75F GLY* 1.3 74.7 - - - +
77F ALA* 1.3 63.1 + - - +
78F MET* 4.3 1.6 + - - +
89F ILE* 3.8 8.5 - - - -
141F LEU* 3.6 33.4 - - - -
142F LEU 3.3 8.5 - - - -
143F PHE* 3.6 30.3 - - + -
226F PHE* 4.7 0.4 - - - -
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Residues in contact with ALA 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F ALA* 4.7 10.8 - - + -
38F ILE 5.8 0.2 - - - +
48F LEU* 4.2 23.7 - - + +
49F ALA 5.3 2.0 - - - +
50F VAL* 5.2 2.5 - - + -
66F LYS 3.2 8.5 - - - +
67F ILE* 4.0 15.5 - - + -
76F CYS* 1.3 75.8 - - - +
78F MET* 1.3 61.8 + - - +
140F ALA 4.0 0.3 - - - +
141F LEU* 3.5 1.4 - - - -
142F LEU* 2.8 43.1 + - + +
170F ILE* 4.0 3.6 - - - +
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Residues in contact with MET 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F ALA* 4.8 0.9 - - - +
50F VAL* 4.3 10.0 - - - +
65F GLU* 3.4 25.6 - - + +
66F LYS* 3.0 32.1 + - - +
68F VAL* 3.6 34.5 - - + -
76F CYS 5.1 0.7 - - - +
77F ALA* 1.3 76.5 - - - +
79F SER* 1.3 62.4 + - - +
82F ILE* 4.0 25.3 - - + +
85F ALA* 3.4 28.5 - - + -
86F LYS* 5.3 0.9 - - - -
89F ILE* 4.2 13.9 - - + -
139F VAL* 4.3 1.1 - - + -
140F ALA 3.4 4.3 - - - +
141F LEU* 3.6 17.0 - - + -
170F ILE* 4.4 2.2 - - - -
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Residues in contact with SER 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F ILE* 4.2 5.6 + - - +
34F GLY* 3.5 10.6 - - - -
35F SER* 2.7 28.2 + - - +
37F ALA* 5.1 0.4 - - - -
66F LYS* 6.0 0.7 - - - +
78F MET* 1.3 75.1 - - - +
80F GLY* 1.3 60.8 + - - +
82F ILE* 4.3 4.3 - - - -
139F VAL* 3.3 8.6 - - - +
140F ALA* 2.9 35.1 + - - +
170F ILE* 3.8 24.9 - - - -
171F GLY* 3.6 10.5 - - - -
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Residues in contact with GLY 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F ALA 4.6 9.4 - - - -
31F ILE* 4.8 3.8 - - - -
34F GLY* 3.7 22.6 - - - -
35F SER 4.6 0.6 - - - +
66F LYS* 6.3 0.2 - - - +
79F SER* 1.3 77.9 + - - +
81F LEU* 1.3 66.8 + - - +
82F ILE* 3.3 15.9 + - - +
138F GLY 4.0 4.3 - - - -
139F VAL* 4.8 0.2 - - - -
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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