Contacts of the helix formed by residues 110 - 128 (chain h) 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 PRO 110 (chain h).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76h ILE* 4.5 0.7 - - - -
101h TRP* 3.9 17.7 - - + -
107h TYR* 4.5 12.3 - - + +
108h GLU 3.6 8.1 - - - +
109h ILE* 1.4 92.0 - - + +
111h VAL* 1.3 67.5 + - - +
112h ASP 3.1 1.6 - - - +
113h MET* 3.0 22.0 + - + +
114h LEU* 3.1 9.9 + - - +
144h ASP* 3.4 24.5 - - - +
145h GLU* 5.9 1.1 - - - +
70p THR* 5.8 0.7 - - + -
72p ARG* 4.2 28.0 - - - +
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Residues in contact with VAL 111 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76h ILE* 4.0 22.7 - - + -
109h ILE 3.9 0.8 + - - -
110h PRO* 1.3 73.0 - - - +
112h ASP* 1.3 65.6 + - - +
114h LEU* 3.2 3.3 + - - +
115h CYS* 2.9 23.0 + - - +
140h LEU* 3.7 34.5 - - + +
141h ILE 4.5 0.9 - - - -
142h GLY* 4.0 33.7 - - - +
143h ILE 5.6 2.2 - - - -
144h ASP* 5.0 2.9 + - + +
150h GLN* 4.4 13.2 - - + +
152h TYR* 3.8 24.5 - - + -
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Residues in contact with ASP 112 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110h PRO* 3.1 0.8 - - - +
111h VAL* 1.3 80.4 - - - +
113h MET* 1.3 71.5 + - - +
115h CYS* 3.8 2.4 - - - +
116h LYS* 3.0 27.1 + - - +
150h GLN* 4.6 3.5 + - - +
152h TYR* 3.9 33.7 + - + +
160h TYR* 3.8 23.4 + - - -
60i SER 4.8 7.1 - - - +
69p SER 5.3 0.5 - - - +
70p THR 4.4 5.2 - - - +
72p ARG* 3.5 28.6 + - - +
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Residues in contact with MET 113 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101h TRP* 3.9 29.8 - - + -
109h ILE* 4.5 3.5 - - + +
110h PRO* 3.0 19.8 + - + +
112h ASP* 1.3 89.6 - - - +
114h LEU* 1.3 64.2 + - - +
116h LYS* 3.7 16.4 - - + +
117h ARG* 3.0 24.3 + - - +
66p HIS* 5.8 0.4 - - + +
69p SER* 3.5 29.6 - - - +
70p THR* 3.3 48.0 - - + -
72p ARG* 5.1 1.8 - - - +
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Residues in contact with LEU 114 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72h ILE* 3.7 25.4 - - + -
76h ILE* 4.0 26.2 - - + -
94h ALA* 3.7 25.1 - - + +
97h GLU* 4.5 9.6 - - + -
98h ALA* 4.6 2.0 - - + -
109h ILE* 3.9 24.1 - - + +
110h PRO 3.1 9.8 + - - +
111h VAL* 3.2 7.8 + - - +
113h MET* 1.3 76.5 - - - +
115h CYS* 1.3 63.4 + - - +
117h ARG* 3.0 4.7 + - + +
118h ILE* 3.0 37.2 + - + +
140h LEU* 4.0 15.7 - - + -
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Residues in contact with CYS 115 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111h VAL 2.9 15.1 + - - +
112h ASP 3.8 2.9 - - - +
114h LEU* 1.3 77.0 - - - +
116h LYS* 1.3 64.1 + - - +
118h ILE* 3.3 6.1 + - - +
119h ALA* 3.0 24.9 + - - +
138h MET 5.1 0.2 - - - -
140h LEU* 3.8 18.5 - - + +
152h TYR* 3.9 13.0 - - + -
153h LYS* 3.7 25.4 - - - -
154h CYS* 3.6 31.9 - - - -
160h TYR* 3.7 14.1 - - + -
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Residues in contact with LYS 116 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112h ASP* 3.0 17.7 + - - +
113h MET* 3.7 22.9 - - + +
114h LEU 3.3 0.2 - - - -
115h CYS* 1.3 75.9 - - - +
117h ARG* 1.3 58.6 + - - +
119h ALA* 3.5 1.7 + - - +
120h ASP* 3.0 45.6 + - - +
160h TYR* 3.6 41.8 + - + +
65i GLU* 4.9 10.3 + - - -
83i ARG* 4.0 14.6 - - - +
90i ARG* 4.7 8.3 - - - +
69p SER* 3.4 36.8 + - - +
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Residues in contact with ARG 117 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93h ARG* 4.1 10.5 - - - +
97h GLU* 3.0 53.3 + - + +
109h ILE* 6.1 0.9 - - + -
113h MET 3.0 19.0 + - - +
114h LEU* 3.0 6.5 + - - +
116h LYS* 1.3 73.7 - - - +
118h ILE* 1.3 65.1 + - + +
120h ASP* 3.2 18.3 + - - +
121h ILE* 3.0 43.3 + - + +
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Residues in contact with ILE 118 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90h GLN* 3.7 38.1 - - + +
93h ARG* 4.3 3.8 - - + +
94h ALA* 3.6 37.2 - - + +
97h GLU* 4.6 3.6 - - + -
114h LEU* 3.0 30.8 + - + +
115h CYS* 3.7 6.5 - - - +
117h ARG* 1.3 75.6 - - - +
119h ALA* 1.3 64.9 + - - +
121h ILE* 3.0 22.3 + - + +
122h SER* 3.0 26.8 + - - +
138h MET* 4.2 10.3 - - - -
154h CYS* 3.9 16.8 - - - -
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Residues in contact with ALA 119 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115h CYS 3.0 18.2 + - - +
116h LYS 3.6 4.9 - - - +
118h ILE* 1.3 78.0 - - - +
120h ASP* 1.3 58.5 + - - +
122h SER* 3.2 4.4 + - - -
123h GLN* 2.9 25.5 + - - +
154h CYS* 4.3 9.4 - - + -
155h ASP 5.4 0.9 - - - -
158h GLY* 3.6 35.9 - - - +
160h TYR* 4.1 16.2 - - + -
83i ARG* 3.9 6.7 - - - +
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Residues in contact with ASP 120 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116h LYS* 3.0 35.4 + - - +
117h ARG* 3.5 17.6 - - - +
119h ALA* 1.3 77.2 - - - +
121h ILE* 1.3 62.4 + - - +
123h GLN* 3.5 17.5 + - - +
124h VAL* 3.7 10.0 + - - +
83i ARG* 2.1 48.9 + - - +
84i VAL* 4.7 11.3 - - + +
87i HIS* 5.7 6.2 - - - +
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Residues in contact with ILE 121 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93h ARG* 3.4 63.7 - - + +
97h GLU* 4.0 9.9 - - + +
117h ARG* 3.0 28.2 + - - +
118h ILE* 3.0 18.6 + - + +
120h ASP* 1.3 77.7 - - - +
122h SER* 1.3 67.8 + - - +
124h VAL* 3.1 23.8 + - + +
125h TYR* 3.7 25.9 + - + +
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Residues in contact with SER 122 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90h GLN* 3.4 24.2 + - - +
118h ILE* 3.0 15.9 + - - +
119h ALA* 3.9 4.5 - - - -
121h ILE* 1.3 79.0 - - - +
123h GLN* 1.3 65.5 + - - +
125h TYR* 2.9 33.6 + - - +
126h THR* 3.1 12.0 + - - -
133h PRO* 6.4 0.2 - - - -
134h LEU* 5.0 5.1 - - - +
155h ASP 4.5 15.0 - - - -
156h PRO* 4.6 10.3 - - - +
157h ALA 4.2 2.7 - - - -
158h GLY* 5.1 0.4 - - - -
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Residues in contact with GLN 123 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119h ALA 2.9 13.3 + - - +
120h ASP* 3.5 14.7 - - - +
121h ILE 3.2 0.4 - - - -
122h SER* 1.3 74.5 - - - +
124h VAL* 1.3 75.0 + - - +
126h THR* 3.0 7.2 + - + -
127h GLN* 2.6 49.1 + - - +
157h ALA 3.5 15.8 + - - +
158h GLY* 4.7 0.4 - - - -
80i PRO* 3.7 27.8 - - + +
81i ASP* 3.0 23.1 + - - +
83i ARG* 5.0 1.3 - - - +
84i VAL* 3.4 29.7 - - + +
127i ARG* 4.1 0.2 - - - +
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Residues in contact with VAL 124 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120h ASP 3.7 7.4 + - - +
121h ILE* 3.1 14.3 + - - +
122h SER 3.0 0.6 - - - -
123h GLN* 1.3 88.9 - - - +
125h TYR* 1.3 70.1 + - + +
127h GLN* 3.0 2.8 + - - +
128h ASN* 2.8 55.2 + - - +
131h MET* 4.3 9.2 - - + -
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Residues in contact with TYR 125 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14h THR* 3.9 7.6 - - - +
93h ARG* 5.0 5.0 + - - -
121h ILE* 4.0 25.1 - - + +
122h SER* 2.9 25.3 + - - +
124h VAL* 1.3 84.3 - - + +
126h THR* 1.3 60.9 + - - +
128h ASN 3.3 14.6 - - - +
131h MET* 3.5 48.0 - - + +
132h ARG 4.4 7.0 - - - -
133h PRO* 3.9 23.6 - - + +
134h LEU* 4.0 35.9 - - + +
124n LEU* 5.6 7.7 - - + +
125n TYR* 5.2 8.6 + + - -
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Residues in contact with THR 126 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416K PHE* 6.1 0.7 - - + -
14h THR* 3.2 24.3 - - - -
22h LEU* 4.0 13.5 - - + +
25h VAL* 3.9 9.0 - - + +
122h SER 3.1 3.1 + - - -
123h GLN* 3.0 13.7 + - + +
125h TYR* 1.3 80.7 - - - +
127h GLN* 1.3 49.9 + - - +
133h PRO* 4.5 2.8 - - - +
156h PRO 3.8 5.0 + - - -
157h ALA* 2.8 41.3 + - + +
78i MET* 5.0 5.4 - - - -
80i PRO* 5.5 1.3 - - + -
81i ASP* 4.5 3.8 - - - +
127i ARG* 2.7 55.8 + - - +
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Residues in contact with GLN 127 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14h THR* 4.2 2.6 + - - +
123h GLN* 2.6 42.1 + - - +
124h VAL* 3.0 3.8 + - - +
126h THR* 1.3 76.7 - - - +
128h ASN* 1.3 68.2 + - - +
84i VAL* 5.0 2.8 - - - +
120i TYR* 2.9 46.4 + - + -
126i VAL* 3.5 5.9 - - + -
127i ARG* 3.2 55.4 + - + +
128i PRO 4.5 0.8 - - - -
129i PHE* 3.5 29.2 - - - +
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Residues in contact with ASN 128 (chain h).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14h THR* 3.0 13.1 + - - -
124h VAL* 2.8 42.3 + - - +
125h TYR 3.3 11.6 - - - +
127h GLN* 1.3 88.3 - - - +
129h ALA* 1.3 65.5 + - - +
130h GLU* 3.4 26.9 + - - +
131h MET* 3.5 16.3 - - - +
120i TYR* 5.9 0.2 - - - -
124i GLY 5.2 1.4 + - - -
125i GLY 3.5 2.7 - - - -
126i VAL* 3.7 19.1 - - - +
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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