Contacts of the strand formed by residues 97 - 111 (chain X) in PDB entry 2Q4G
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 TYR 97 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23X SER 5.3 3.3 - - - +
26X CYS* 3.7 18.8 - - + -
27X ASN* 2.8 33.5 + - - +
30X MET* 3.5 41.7 - - + +
36X THR* 3.5 11.0 - - + +
40X CYS* 3.8 4.7 - - - +
41X LYS 2.6 42.1 + - - -
42X PRO 4.0 5.8 - - - -
84X CYS* 4.1 13.2 - - + -
85X ARG 3.1 6.5 - - - +
86X LEU* 3.7 28.3 - - + -
87X THR* 4.3 6.2 - - - +
95X CYS* 3.8 20.6 - - + -
96X ALA* 1.3 75.9 - - - +
98X ARG* 1.3 61.7 + - - +
99X THR* 4.0 3.1 + - - -
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Residues in contact with ARG 98 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83X ASP* 3.5 3.9 - - - +
84X CYS* 3.3 5.5 - - - -
85X ARG* 2.7 92.9 + - - +
86X LEU 5.5 0.6 + - - -
87X THR* 4.4 8.0 - - + +
97X TYR* 1.3 74.1 - - - +
99X THR* 1.3 63.9 + - - +
100X SER* 3.3 25.0 + - - +
102X LYS* 6.0 1.0 - - - +
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Residues in contact with THR 99 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X SER* 3.6 14.8 - - - +
22X SER 3.5 26.3 + - - +
23X SER* 4.4 10.8 + - - +
25X TYR* 4.0 3.3 + - + -
26X CYS* 3.0 34.2 + - - +
27X ASN 4.6 0.5 + - - -
82X THR* 3.4 25.8 - - + -
97X TYR 4.0 2.2 + - - -
98X ARG* 1.3 74.4 - - - +
100X SER* 1.3 61.5 + - - +
101X PRO* 3.6 8.1 - - + +
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Residues in contact with SER 100 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82X THR* 3.3 1.6 - - - -
83X ASP* 2.6 52.2 + - - +
98X ARG* 3.3 34.0 + - - +
99X THR* 1.3 75.2 + - - +
101X PRO* 1.3 64.5 - - - +
102X LYS* 3.8 18.6 - - - +
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Residues in contact with PRO 101 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19X PRO 3.6 24.2 - - - +
20X SER* 4.5 5.8 - - - -
21X SER* 3.8 19.7 - - - +
81X ILE 3.4 7.4 - - - +
82X THR* 3.7 9.4 - - - +
99X THR* 3.6 15.0 - - + +
100X SER* 1.3 85.2 - - - +
102X LYS* 1.3 66.2 + - - +
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Residues in contact with LYS 102 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80X HIS* 3.5 3.3 - - - +
81X ILE* 2.7 53.4 + - + +
83X ASP* 2.7 32.9 + - - +
85X ARG* 5.5 4.6 - - - +
98X ARG* 6.0 0.8 - - - +
100X SER* 3.8 23.3 - - - +
101X PRO* 1.3 76.3 - - - +
103X GLU* 1.3 61.6 + - - +
104X ARG* 3.7 45.8 - - + +
123X SER* 5.2 0.9 - - - +
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Residues in contact with GLU 103 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78X SER* 3.9 20.7 + - - +
79X MET 3.2 6.7 - - - +
80X HIS* 3.1 40.2 - - - +
102X LYS* 1.3 78.6 - - - +
104X ARG* 1.3 86.2 + - - +
127X SER* 5.0 4.7 + - - -
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Residues in contact with ARG 104 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78X SER* 3.4 10.5 - - - -
79X MET* 2.6 35.7 + - - +
81X ILE* 4.3 6.4 - - + +
102X LYS* 3.7 44.8 - - + +
103X GLU* 1.3 108.6 + - - +
105X HIS* 1.3 66.2 + - - +
106X ILE* 3.8 3.1 + - - +
123X SER* 3.8 15.5 - - - +
124X VAL 3.3 11.7 - - - +
125X GLU* 3.7 49.3 + - - +
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Residues in contact with HIS 105 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74X LYS* 3.9 23.5 - - + -
75X SER* 3.0 30.0 + - - +
76X ASN 3.0 25.3 + - - -
77X SER* 3.7 7.0 - - - -
78X SER* 3.4 23.1 + - - -
104X ARG* 1.3 76.1 - - - +
106X ILE* 1.3 59.3 + - - +
123X SER* 3.1 6.4 - - - -
124X VAL* 2.8 40.5 + - + +
126X ASP* 3.2 32.6 + - - -
127X SER* 4.9 5.7 - - - -
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Residues in contact with ILE 106 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47X VAL* 4.5 3.1 - - + -
54X VAL* 3.8 23.1 - - + -
57X VAL* 4.2 11.7 - - + -
73X TYR 3.6 0.2 - - - +
74X LYS* 3.2 5.2 - - - +
75X SER* 3.0 41.2 + - - +
79X MET* 4.0 20.0 - - - -
81X ILE* 4.1 20.0 - - + -
104X ARG 4.4 1.6 - - - +
105X HIS* 1.3 78.1 - - - +
107X ILE* 1.3 63.1 + - - +
108X VAL* 3.4 26.9 - - + -
120X PHE* 3.7 31.6 - - + -
122X ALA 3.5 4.0 - - - -
123X SER* 5.2 0.9 - - - -
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Residues in contact with ILE 107 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63X VAL* 3.9 18.4 - - + -
64X THR 4.8 4.5 - - - +
72X CYS* 4.1 8.7 - - + -
73X TYR 3.0 10.5 - - - +
74X LYS* 4.1 19.3 - - + -
106X ILE* 1.3 78.9 - - - +
108X VAL* 1.3 55.0 + - - +
120X PHE* 4.2 1.0 - - - -
121X ASP* 2.7 53.2 + - + +
122X ALA* 2.7 28.4 + - + +
124X VAL* 3.5 32.3 - - + -
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Residues in contact with VAL 108 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X PHE* 4.1 20.4 - - + -
54X VAL* 4.8 1.3 - - + +
57X VAL* 4.1 24.5 - - + -
72X CYS* 3.5 6.6 - - - -
73X TYR* 2.9 28.8 + - + +
106X ILE* 3.4 27.1 - - + -
107X ILE* 1.3 77.0 - - - +
109X ALA* 1.3 61.7 + - - +
110X CYS* 3.8 21.8 - - - -
117X PRO* 4.5 10.8 - - + -
119X HIS 3.2 13.9 - - - +
120X PHE* 4.4 8.3 - - + -
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Residues in contact with ALA 109 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437W TYR* 3.3 42.4 - - + +
65X CYS* 4.2 0.2 - - - -
71X ASN 4.2 2.7 - - - +
72X CYS* 3.8 10.5 - - - -
108X VAL* 1.3 75.1 - - - +
110X CYS* 1.3 55.5 + - - +
117X PRO* 3.2 4.7 - - - +
118X VAL* 2.5 33.9 + - + -
119X HIS* 2.9 24.6 + - + -
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Residues in contact with CYS 110 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58X CYS* 2.0 60.8 - - + -
71X ASN* 3.9 13.3 + - - +
73X TYR* 3.8 10.7 - - + -
108X VAL* 3.8 10.5 + - - -
109X ALA* 1.3 80.1 - - - +
111X GLU* 1.3 71.0 + - - +
115X TYR* 3.2 29.7 + - + -
116X VAL 3.0 7.4 - - - +
117X PRO* 3.8 4.3 - - - -
118X VAL* 3.9 0.4 - - - -
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Residues in contact with GLU 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437W TYR* 2.8 34.7 + - - +
438W TRP 4.2 2.4 - - - +
439W SER* 4.2 11.1 - - - -
440W GLU* 2.4 51.8 + - + +
4X ARG* 4.6 0.9 + - - -
71X ASN* 4.0 4.5 + - - +
110X CYS* 1.3 81.4 - - - +
112X GLY* 1.3 64.2 + - - +
114X PRO 3.7 2.1 - - - +
115X TYR* 3.5 10.3 - - - -
116X VAL* 3.0 32.8 + - - +
118X VAL* 3.3 20.3 - - + +
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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
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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