Contacts of the helix formed by residues 107 - 121 (chain n) 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 107 (chain n).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98n PHE* 3.6 17.3 - - + -
104n TYR* 4.1 9.9 - - + -
105n ASN 3.4 5.1 - - - +
106n ILE* 1.3 96.7 - - + +
108n LEU* 1.3 65.8 + - - +
109n LYS* 4.5 4.3 - - + +
110n HIS* 3.2 12.3 + - + +
111n LEU* 3.1 18.0 + - - +
144n ASP* 5.6 6.7 - - - +
147n GLN* 6.2 0.2 - - - +
70o LEU* 3.8 33.9 - - + -
72o GLU* 5.3 6.7 - - - +
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Residues in contact with LEU 108 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72n HIS* 5.7 0.4 - - - -
73n VAL* 3.6 40.6 - - + -
106n ILE 3.6 3.5 + - - -
107n PRO* 1.3 72.5 - - - +
109n LYS* 1.3 64.2 + - - +
111n LEU* 3.2 8.4 + - + +
112n ALA* 2.9 23.8 + - - +
137n LEU* 3.5 27.6 - - + +
138n GLY 4.3 0.9 - - - -
139n SER* 3.6 20.5 + - - +
147n GLN* 3.3 52.5 - - + +
149n TYR* 4.0 12.3 - - + -
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Residues in contact with LYS 109 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107n PRO* 3.3 4.6 - - + +
108n LEU* 1.3 78.5 - - - +
110n HIS* 1.3 57.5 + - - +
112n ALA* 3.5 2.5 + - - +
113n ASP* 2.9 34.4 + - - +
147n GLN* 4.0 11.8 - - - +
149n TYR* 3.4 33.0 - - + +
70o LEU* 5.9 2.5 - - + -
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Residues in contact with HIS 110 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94n GLU* 5.5 1.3 - - - -
98n PHE* 3.3 37.7 - + - -
102n PHE* 5.7 1.3 - + - -
106n ILE* 3.6 9.0 - - + +
107n PRO* 3.2 15.2 + - + +
108n LEU 3.1 0.6 - - - -
109n LYS* 1.3 76.3 - - - +
111n LEU* 1.3 66.5 + - - +
113n ASP* 3.2 11.5 + - + +
114n ARG* 3.0 47.1 + - + +
66o HIS* 4.7 4.6 - + - -
69o GLU* 3.3 46.1 + - + +
70o LEU* 3.7 27.9 - - + +
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Residues in contact with LEU 111 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69n VAL* 3.7 23.6 - - + -
73n VAL* 3.8 27.6 - - + -
91n ALA* 3.6 25.1 - - + +
94n GLU* 4.1 11.9 - - + -
95n ALA* 4.4 5.6 - - + +
106n ILE* 3.8 23.4 - - + +
107n PRO 3.1 9.5 + - - +
108n LEU* 3.2 10.5 + - + +
110n HIS* 1.3 78.3 - - - +
112n ALA* 1.3 63.6 + - - +
114n ARG* 3.3 1.9 + - - +
115n VAL* 3.0 44.5 + - + +
137n LEU* 4.3 13.0 - - + -
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Residues in contact with ALA 112 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108n LEU 2.9 17.5 + - - +
109n LYS 3.6 4.0 - - - +
111n LEU* 1.3 78.6 - - - +
113n ASP* 1.3 63.3 + - - +
115n VAL* 4.2 0.7 - - - +
116n ALA* 2.9 28.9 + - - +
137n LEU* 4.1 15.7 - - + +
149n TYR* 4.1 26.2 - - + -
151n ILE* 4.7 5.1 - - + +
157n SER* 3.8 17.7 - - - +
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Residues in contact with ASP 113 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88h ARG* 4.8 13.5 - - - -
92h GLN* 5.3 13.6 + - + +
95h ARG* 5.5 1.8 + - - -
109n LYS* 2.9 23.8 + - - +
110n HIS* 3.2 20.0 + - + +
112n ALA* 1.3 72.1 - - - +
114n ARG* 1.3 59.7 + - + +
116n ALA* 3.8 4.0 - - - +
117n MET* 3.0 36.6 + - + +
157n SER* 4.7 2.8 + - - -
69o GLU* 4.1 17.9 - - - +
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Residues in contact with ARG 114 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92h GLN* 5.1 5.2 + - - -
94n GLU* 2.7 53.8 + - + +
110n HIS* 3.0 44.9 + - + +
111n LEU* 3.8 1.6 - - - +
113n ASP* 1.3 77.4 - - - +
115n VAL* 1.3 67.9 + - - +
117n MET* 3.2 9.1 + - - +
118n TYR* 3.0 22.5 + - - +
65o PHE* 6.2 0.6 - - - -
69o GLU* 4.1 14.7 + - - -
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Residues in contact with VAL 115 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87n LEU* 4.9 14.4 - - + +
90n ILE* 4.7 8.3 - - + -
91n ALA* 3.9 21.1 - - + +
94n GLU* 4.8 4.5 - - + -
111n LEU* 3.0 37.4 + - + +
112n ALA* 4.2 3.6 - - - +
114n ARG* 1.3 75.6 - - - +
116n ALA* 1.3 57.3 - - - +
118n TYR* 3.2 8.1 + - - +
119n VAL* 2.9 31.9 + - + +
135n PHE* 3.4 36.1 - - + -
137n LEU* 5.3 2.2 - - + -
151n ILE* 5.6 0.7 - - + -
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Residues in contact with ALA 116 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112n ALA 2.9 19.6 + - - +
113n ASP* 3.8 3.6 - - - +
115n VAL* 1.3 76.1 - - - +
117n MET* 1.3 60.0 + - - +
119n VAL* 3.7 5.8 - - - +
120n HIS* 2.9 30.0 + - - +
151n ILE* 4.2 11.9 - - + -
155n GLY* 3.4 24.6 - - - +
157n SER* 3.8 19.7 - - - -
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Residues in contact with MET 117 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85h ALA 5.0 1.3 - - - +
88h ARG* 3.9 11.9 - - + +
89h SER* 3.2 54.7 - - - +
92h GLN* 4.2 22.0 - - + -
113n ASP* 3.0 23.4 + - + +
114n ARG* 3.5 7.0 - - - +
116n ALA* 1.3 77.6 - - - +
118n TYR* 1.3 63.2 + - - +
120n HIS* 3.3 10.7 + - - +
121n ALA* 3.0 21.3 + - - +
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Residues in contact with TYR 118 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122m ARG* 5.6 1.4 + - - -
87n LEU* 4.4 4.5 - - + -
90n ILE* 3.4 51.7 - - + +
114n ARG 3.0 13.0 + - - +
115n VAL* 3.4 11.4 - - - +
117n MET* 1.3 79.1 - - - +
119n VAL* 1.3 62.4 + - - +
121n ALA* 3.2 21.9 + - + +
122n TYR* 3.3 42.7 + + - -
131n PHE* 4.1 11.2 - + - -
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Residues in contact with VAL 119 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87n LEU* 3.8 37.2 - - + -
115n VAL* 2.9 26.1 + - + +
116n ALA* 3.7 6.1 - - - +
118n TYR* 1.3 72.1 - - - +
120n HIS* 1.3 66.8 + - - +
122n TYR* 3.1 19.8 + - - +
123n THR* 4.0 5.4 - - - +
131n PHE* 4.1 17.8 + - + -
135n PHE* 4.5 0.4 - - + -
151n ILE* 4.4 9.9 - - + -
152n ASP 3.7 17.5 - - - +
153n PRO* 3.6 24.6 - - + +
155n GLY* 4.0 4.3 - - - +
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Residues in contact with HIS 120 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85h ALA* 3.6 23.1 - - + +
86h ASP* 3.0 34.5 + - - -
89h SER* 3.1 34.7 + - - -
134h LEU* 4.6 3.1 - - + -
116n ALA 2.9 18.0 + - - +
117n MET* 3.6 11.3 + - - +
118n TYR 3.3 0.2 - - - -
119n VAL* 1.3 78.3 - - - +
121n ALA* 1.3 60.0 + - - +
122n TYR 3.0 4.1 + - - -
123n THR* 2.9 29.2 + - - -
124n LEU* 3.8 32.3 - - + +
154n SER 3.7 15.5 - - - +
155n GLY* 4.0 3.8 - - - +
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Residues in contact with ALA 121 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1i ALA 3.5 20.4 + - - +
117n MET 3.0 12.9 + - - +
118n TYR* 3.2 19.5 - - + +
119n VAL 3.0 1.0 - - - -
120n HIS* 1.3 76.9 - - - +
122n TYR* 1.3 65.2 + - + +
123n THR 3.3 0.7 - - - -
124n LEU* 4.2 12.5 + - + -
125n TYR* 3.6 17.7 - - + -
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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