Contacts of the strand formed by residues 88 - 106 (chain V) in PDB entry 2FJG
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 GLY 88 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32H TYR* 5.9 0.2 - - - -
102H PHE* 3.3 20.8 - - - +
84V LYS* 2.8 34.6 + - - +
87V GLN* 1.3 81.2 - - - +
89V GLN* 1.3 63.0 + - - +
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Residues in contact with GLN 89 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H ASP* 3.0 28.2 - - - +
32H TYR* 3.6 41.8 + - + -
99H PHE 4.7 0.7 - - - +
100H VAL* 4.6 1.2 - - - -
101H PHE* 2.9 39.8 + - - +
102H PHE* 3.0 21.6 - - + +
81V MET* 3.5 17.9 - - - +
82V ARG 3.4 5.8 - - - +
83V ILE* 3.8 16.6 - - + -
88V GLY* 1.3 74.6 - - - +
90V HIS* 1.3 61.6 + - - +
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Residues in contact with HIS 90 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H ASP* 3.5 19.0 + - - -
228H SO4 4.9 11.9 + - - -
81V MET* 4.0 6.0 - - - +
82V ARG* 2.9 48.6 + - - +
89V GLN* 1.3 75.4 + - - +
91V ILE* 1.3 91.2 + - - +
92V GLY* 3.3 5.8 + - - -
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Residues in contact with ILE 91 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H SER* 3.4 26.2 - - - +
31H ASP* 3.6 15.2 + - - +
79V GLN* 3.9 37.5 - - + +
80V ILE 3.4 9.0 - - - +
81V MET* 3.3 25.6 - - + +
90V HIS* 1.3 87.0 + - - +
92V GLY* 1.3 59.7 + - - +
17W PHE* 3.8 34.3 - - + -
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Residues in contact with GLY 92 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79V GLN* 3.5 3.3 - - - -
80V ILE* 2.8 37.1 + - - +
82V ARG* 4.7 14.0 - - - +
90V HIS* 3.3 9.7 + - - -
91V ILE* 1.3 75.0 - - - +
93V GLU* 1.3 66.5 + - - -
94V MET* 3.8 3.0 + - - -
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Residues in contact with GLU 93 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77V THR* 3.6 26.2 - - + +
78V MET 3.4 4.5 - - - +
79V GLN* 4.5 20.8 + - + +
82V ARG* 6.1 0.3 - - - -
92V GLY* 1.3 72.3 - - - -
94V MET* 1.3 64.1 + - - +
14W VAL* 4.4 16.9 - - + +
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Residues in contact with MET 94 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35V ILE* 3.8 11.7 - - + -
39V TYR* 3.7 38.4 - - + +
42V GLU* 4.5 4.9 - - - +
47V PHE* 3.5 38.8 - - + -
77V THR* 3.5 4.3 - - - -
78V MET 3.0 29.9 + - - +
80V ILE* 3.8 28.7 - - + -
82V ARG* 4.9 11.2 - - - -
92V GLY 4.8 1.8 - - - +
93V GLU* 1.3 77.7 - - - +
95V SER* 1.3 61.8 + - - +
96V PHE* 3.7 21.2 - - + -
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Residues in contact with SER 95 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39V TYR* 2.9 35.6 + - - -
75V ASN* 2.9 31.5 + - - +
76V ILE 3.7 3.8 - - - -
77V THR* 4.0 14.1 - - - -
94V MET* 1.3 73.7 - - - +
96V PHE* 1.3 62.8 + - - +
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Residues in contact with PHE 96 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35V ILE* 3.9 29.8 - - + -
38V GLU* 4.3 20.6 - - + -
39V TYR* 4.1 19.3 - + - -
52V VAL* 4.1 19.1 - - + -
54V LEU* 3.7 24.5 - - + -
75V ASN* 3.4 9.3 - - - +
76V ILE* 3.0 37.0 + - + +
78V MET* 4.0 25.8 - - + -
80V ILE* 4.3 4.7 - - + -
94V MET* 3.7 39.3 - - + -
95V SER* 1.3 77.9 + - - +
97V LEU* 1.3 62.3 + - - +
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Residues in contact with LEU 97 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38V GLU* 4.9 5.3 + - - +
54V LEU* 3.7 5.0 - - - +
56V ARG* 2.6 35.9 + - - +
73V GLU* 3.6 49.6 - - + +
74V SER 4.0 7.0 - - - +
75V ASN* 4.2 17.4 - - - +
96V PHE* 1.3 75.7 - - - +
98V GLN* 1.3 67.6 + - - +
99V HIS* 4.4 10.3 - - + -
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Residues in contact with GLN 98 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53V PRO 4.1 4.5 - - - +
54V LEU* 3.7 9.3 - - + -
55V MET* 3.2 43.3 + - + +
73V GLU* 3.4 6.2 - - - +
74V SER* 2.9 43.1 + - - +
75V ASN 5.2 1.2 + - - -
76V ILE* 3.6 49.6 - - + +
97V LEU* 1.3 79.0 - - - +
99V HIS* 1.3 70.4 + - - +
100V ASN* 4.1 0.9 - - - +
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Residues in contact with HIS 99 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28V PRO* 3.4 19.4 - - - +
55V MET* 2.7 23.7 + - - +
56V ARG* 3.9 25.3 + - + +
57V CYS* 3.3 54.1 - - + +
70V PRO* 3.4 22.2 - - + +
72V GLU 3.8 3.6 - - - -
73V GLU* 3.9 19.0 - - - +
97V LEU* 4.4 13.5 - - + -
98V GLN* 1.3 80.5 + - - +
100V ASN* 1.3 62.7 + - - +
102V CYS* 4.4 2.0 - - - -
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Residues in contact with ASN 100 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28V PRO* 3.3 15.3 - - - +
72V GLU* 2.8 29.9 + - + +
73V GLU* 3.0 25.7 + - - +
74V SER* 2.4 33.8 + - - +
98V GLN* 5.8 0.7 - - - +
99V HIS* 1.3 75.1 - - - +
101V LYS* 1.3 72.2 + - + +
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Residues in contact with LYS 101 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28V PRO* 4.4 1.8 - - - -
57V CYS* 3.9 0.2 - - - -
70V PRO* 3.4 4.9 - - - +
71V THR* 3.1 37.7 + - - +
72V GLU* 3.5 33.7 + - + +
100V ASN* 1.3 89.9 + - + +
102V CYS* 1.3 74.6 + - - +
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Residues in contact with CYS 102 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26V CYS* 3.7 19.3 - - - -
27V HIS* 3.7 10.1 - - - -
28V PRO* 3.6 24.6 - - - +
57V CYS* 2.0 54.7 - - - -
69V VAL 3.5 6.3 - - - +
71V THR* 4.3 1.9 + - - +
99V HIS* 4.4 2.2 - - - -
101V LYS* 1.3 82.0 - - - +
103V GLU* 1.3 72.4 + - - +
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Residues in contact with GLU 103 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25V TYR* 6.1 1.6 - - - -
26V CYS* 3.6 9.0 - - - -
67V GLU 3.5 0.3 - - - +
68V CYS* 3.8 0.2 - - - -
69V VAL* 3.2 27.9 + - - +
71V THR* 3.5 19.9 - - + +
102V CYS* 1.3 84.8 - - - +
104V CYS* 1.3 64.1 + - - +
105V ARG* 3.5 38.8 + - + +
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Residues in contact with CYS 104 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A THR* 5.0 10.4 - - - +
25V TYR* 3.3 27.9 + - - +
26V CYS* 3.5 18.6 - - - -
61V CYS* 2.0 51.8 - - + -
66V LEU* 3.9 18.7 - - + +
67V GLU 3.2 4.3 - - - -
103V GLU* 1.3 74.5 - - - +
105V ARG* 1.3 61.4 + - - +
106V PRO* 4.6 1.7 - - - +
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Residues in contact with ARG 105 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66V LEU* 3.9 3.4 - - - -
67V GLU* 2.9 37.2 + - - +
69V VAL* 3.7 28.1 - - + +
70V PRO 5.8 0.6 + - - -
71V THR* 4.6 13.3 - - - +
103V GLU* 3.5 28.0 + - - +
104V CYS* 1.3 76.3 - - - +
106V PRO* 1.3 77.0 - - + +
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Residues in contact with PRO 106 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ASP* 3.7 50.0 - - + +
29A VAL* 5.9 0.2 - - - -
30A SER* 5.2 2.5 - - - +
65V GLY 4.0 1.3 - - - +
66V LEU* 3.7 21.2 - - + +
67V GLU* 3.5 4.3 - - - +
104V CYS 4.6 1.8 - - - +
105V ARG* 1.3 99.9 - - + +
107V LYS* 1.3 62.6 + - - +
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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