Contacts of the helix formed by residues 92 - 110 (chain X) in PDB entry 5G04
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 92 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54X ARG* 3.9 24.6 + - - -
87X LEU* 3.1 13.5 + - + +
90X ASP* 4.1 15.7 - - + +
91X LYS* 1.3 75.9 - - - +
93X TYR* 1.3 62.6 - - - +
94X ARG 3.4 2.5 - - - -
95X ASN* 3.4 25.5 + - + +
96X ALA* 3.1 21.9 + - - +
303Y TYR* 5.1 8.8 - - + +
305Y ILE* 4.0 38.7 + - + +
334Y ILE 5.9 0.4 - - - -
335Y SER* 5.6 4.5 - - - -
338Y HIS* 4.4 9.1 - - + +
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Residues in contact with TYR 93 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88X PHE* 3.6 37.9 + + - -
91X LYS* 3.2 49.7 + - + +
92X GLU* 1.3 70.0 - - - +
94X ARG* 1.3 66.4 + - - +
96X ALA* 3.2 5.9 + - - +
97X VAL* 2.9 29.9 + - - +
145X CYS* 4.0 12.3 - - + +
148X MET* 3.2 52.1 - - + +
149X LEU* 3.5 24.9 - - + -
334Y ILE 5.5 0.6 + - - -
335Y SER* 5.8 2.6 - - - -
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Residues in contact with ARG 94 (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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520H ARG* 3.7 35.3 + - - +
527H ARG* 4.1 19.4 - - - +
548H LYS* 5.9 2.8 - - - +
92X GLU 3.4 0.2 - - - -
93X TYR* 1.3 77.2 - - - +
95X ASN* 1.3 61.9 + - - +
97X VAL* 3.6 6.4 + - - +
98X SER* 3.3 23.9 + - - -
146X TYR* 5.8 0.2 - - - -
149X LEU* 4.0 21.6 - - + +
151X GLN* 3.3 34.0 + - - +
303Y TYR* 4.1 17.2 + - + -
333Y ASN* 3.9 15.1 + - - +
334Y ILE* 3.0 34.5 + - - +
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Residues in contact with ASN 95 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83X HIS* 4.7 2.4 + - - -
87X LEU* 3.0 38.8 - - + +
92X GLU* 3.4 22.4 + - + +
93X TYR 3.2 0.2 - - - -
94X ARG* 1.3 77.8 - - - +
96X ALA* 1.3 65.0 + - - +
98X SER* 3.1 4.3 + - - -
99X LYS* 3.1 33.9 + - - +
301Y ASP* 4.9 4.9 + - - +
303Y TYR* 3.4 45.8 + - + +
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Residues in contact with ALA 96 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84X ALA 4.2 5.6 - - - +
87X LEU* 3.9 11.8 - - + +
88X PHE* 4.0 22.2 - - + +
92X GLU 3.1 11.5 + - - +
93X TYR* 3.5 9.4 - - - +
95X ASN* 1.3 79.9 - - - +
97X VAL* 1.3 57.3 + - - +
99X LYS* 3.2 3.0 + - - +
100X TYR* 2.9 38.8 + - + -
145X CYS* 4.0 19.1 - - - -
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Residues in contact with VAL 97 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520H ARG* 4.1 15.9 - - - +
524H GLU* 5.8 0.4 - - - +
93X TYR 2.9 21.5 + - - +
94X ARG* 3.8 7.2 - - - +
96X ALA* 1.3 77.3 - - - +
98X SER* 1.3 58.6 + - - +
100X TYR* 3.4 7.8 + - - +
101X THR* 2.9 37.1 + - - +
142X MET* 4.2 11.3 - - + +
145X CYS* 3.5 24.0 - - + -
146X TYR* 3.4 35.4 - - + +
149X LEU* 4.4 15.0 - - + -
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Residues in contact with SER 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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520H ARG* 5.1 3.7 + - - +
524H GLU* 4.7 11.6 - - - +
527H ARG* 4.0 8.3 + - - -
94X ARG 3.3 6.0 + - - -
95X ASN* 3.1 11.0 + - - -
97X VAL* 1.3 78.9 - - - +
99X LYS* 1.3 64.6 + - - +
101X THR* 3.4 7.2 + - - -
102X MET* 3.0 31.8 + - - +
303Y TYR* 3.0 32.7 + - - -
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Residues in contact with LYS 99 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61X LEU* 4.1 16.2 - - - +
80X LEU* 4.0 13.5 - - + +
83X HIS* 3.6 24.3 + - + -
84X ALA* 3.9 16.8 - - + -
87X LEU* 3.3 22.0 - - + -
95X ASN* 3.1 20.8 + - - +
96X ALA 3.2 6.0 + - - +
98X SER* 1.3 74.8 - - - +
100X TYR* 1.3 54.0 + - - +
102X MET* 3.0 30.8 + - + +
103X ALA* 2.7 36.0 + - - +
271Y VAL* 6.2 0.8 - - - +
301Y ASP* 4.7 14.0 + - - -
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Residues in contact with TYR 100 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81X VAL* 4.5 9.0 - - + -
84X ALA* 3.4 29.1 - - + +
85X ASP* 2.6 35.0 + - - -
88X PHE* 4.6 6.8 - - + +
96X ALA* 2.9 35.8 + - + +
97X VAL* 3.6 2.9 - - - +
99X LYS* 1.3 75.8 - - - +
101X THR* 1.3 63.6 + - - +
103X ALA* 2.9 17.5 + - + +
104X LEU* 2.9 18.1 + - - +
138X VAL* 3.1 30.7 - - + -
141X LYS* 3.3 32.4 - - + +
142X MET* 3.2 31.6 - - + -
145X CYS* 4.7 4.9 - - - -
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Residues in contact with THR 101 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496H TYR* 5.2 11.6 - - + +
520H ARG* 5.8 0.2 + - - -
521H ILE* 6.5 1.6 - - + -
524H GLU* 3.7 26.8 + - - +
97X VAL* 2.9 21.3 + - - +
98X SER* 3.7 8.1 - - - -
99X LYS 3.3 0.2 - - - -
100X TYR* 1.3 75.1 - - - +
102X MET* 1.3 63.4 + - + +
104X LEU* 3.4 10.3 + - + +
105X GLN* 3.1 20.8 + - - +
142X MET* 3.3 21.3 - - + +
146X TYR* 5.1 1.0 + - - -
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Residues in contact with MET 102 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493H SER* 5.1 1.6 + - - -
496H TYR* 5.9 2.7 - - + -
497H ASN* 3.9 35.0 - - - +
528H ILE* 5.9 7.0 - - + -
80X LEU* 3.7 19.6 - - + +
98X SER* 3.0 16.1 + - - +
99X LYS* 3.0 52.1 + - + +
101X THR* 1.3 76.5 - - - +
103X ALA* 1.3 62.6 - - - +
105X GLN* 3.2 10.4 + - - +
106X GLN* 3.1 19.8 + - - +
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Residues in contact with ALA 103 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77X TYR* 3.3 13.0 - - + -
80X LEU* 3.5 26.9 - - + +
81X VAL* 4.3 21.3 - - + +
99X LYS 2.7 15.4 + - - +
100X TYR* 3.2 13.9 - - + +
102X MET* 1.3 73.6 - - - +
104X LEU* 1.3 57.5 + - - +
106X GLN* 3.0 8.9 + - - +
107X LYS 2.9 23.2 + - - -
138X VAL* 4.8 5.2 - - + -
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Residues in contact with LEU 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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77X TYR* 5.5 2.5 - - + +
100X TYR 2.9 16.1 + - - +
101X THR* 3.8 9.0 - - + +
102X MET 3.3 0.2 - - - -
103X ALA* 1.3 73.1 - - - +
105X GLN* 1.3 67.4 + - - +
107X LYS* 3.1 9.0 + - - +
108X LYS* 3.1 32.1 + - - +
135X GLU* 4.5 13.7 - - + +
138X VAL* 3.5 35.0 - - + -
139X LYS* 4.2 29.6 - - + -
142X MET* 3.2 30.5 - - + -
158X ILE* 5.2 2.0 - - + -
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Residues in contact with GLN 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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489H SER* 2.9 38.1 + - - +
491H LEU 3.5 12.9 + - - -
493H SER* 3.7 16.0 - - - +
496H TYR* 3.3 66.6 - - + +
497H ASN* 5.1 1.3 - - - +
101X THR 3.1 12.9 + - - +
102X MET* 3.3 10.8 - - - +
104X LEU* 1.3 75.4 - - - +
106X GLN* 1.3 65.1 + - - +
108X LYS* 3.0 18.4 + - - +
109X ALA* 3.0 10.1 + - - +
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Residues in contact with GLN 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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492H PRO 5.1 0.5 - - - +
493H SER* 3.5 24.3 + - - +
497H ASN* 5.8 0.2 + - - -
73X PRO* 4.0 17.7 - - + +
76X LYS* 2.7 49.4 + - - +
77X TYR* 2.8 21.8 - - + +
80X LEU* 4.4 11.4 - - - +
102X MET 3.1 7.6 + - - +
103X ALA* 3.0 12.4 + - - +
105X GLN* 1.3 82.1 - - - +
107X LYS* 1.3 62.1 + - - +
109X ALA* 3.0 12.7 + - + +
110X LEU* 3.0 19.9 + - - +
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Residues in contact with LYS 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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77X TYR* 3.3 41.6 - - + +
103X ALA 2.9 6.4 + - - +
104X LEU* 3.1 13.9 + - + +
106X GLN* 1.3 76.6 - - - +
108X LYS* 1.3 62.6 + - + +
110X LEU* 3.2 17.1 + - - +
133X PRO 5.1 2.6 + - - -
134X SER* 5.9 0.2 - - - +
135X GLU* 4.0 46.9 - - + +
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Residues in contact with LYS 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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485H ILE* 5.3 8.1 - - - +
486H ASN* 5.3 8.5 + - - +
489H SER* 3.9 36.6 + - - +
490H HIS* 3.9 21.0 + - + +
509H TYR* 5.5 3.0 + - - -
104X LEU* 3.1 23.7 + - - +
105X GLN* 3.0 12.6 + - - +
107X LYS* 1.3 75.1 - - + +
109X ALA* 1.3 67.9 + - - +
110X LEU* 3.3 9.4 + - - +
135X GLU* 5.8 5.6 - - - +
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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
----------------------------------------------------------
489H SER 4.2 6.7 + - - +
490H HIS* 4.5 11.9 - - - +
491H LEU 4.0 21.3 - - - +
492H PRO* 5.1 4.3 - - + +
493H SER* 4.8 6.3 - - - -
73X PRO* 6.0 4.0 - - + -
105X GLN* 3.0 11.9 + - - +
106X GLN* 3.0 19.2 + - + +
108X LYS* 1.3 77.3 - - - +
110X LEU* 1.4 72.5 + - - +
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Residues in contact with LEU 110 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490H HIS* 6.2 0.9 - - - +
73X PRO* 4.3 12.0 - - - +
74X PRO* 4.2 27.2 - - - +
106X GLN 3.0 12.4 + - - +
107X LYS* 3.5 12.8 - - - +
108X LYS 3.2 10.4 - - - +
109X ALA* 1.4 83.8 - - - +
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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
------------------------------------------------------------
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