Contacts of the helix formed by residues 117 - 132 (chain G) in PDB entry 5JLH
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 ASN 117 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G GLN* 3.1 43.8 - - + +
98G ARG 3.2 6.9 + - - +
115G CYS* 3.0 29.5 + - - -
116G LEU* 1.3 74.1 - - - +
118G GLU* 1.3 64.5 + - - +
119G ALA* 3.8 0.2 - - - +
120G SER* 2.6 40.8 + - - -
121G VAL* 3.0 24.1 + - - +
725G ILE* 4.0 9.0 - - - +
729G ARG* 4.6 8.1 - - - +
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Residues in contact with GLU 118 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G PHE* 3.6 28.5 - - + -
97G GLN* 3.7 17.0 + - - +
117G ASN* 1.3 73.5 - - - +
119G ALA* 1.3 59.5 + - - +
121G VAL* 3.6 9.0 - - - +
122G LEU* 2.8 32.3 + - - +
713G LEU* 3.4 20.2 - - + +
716G LEU* 5.2 2.3 - - + +
717G ARG* 3.4 26.7 + - - -
722G LEU* 3.7 31.1 - - + +
725G ILE* 4.0 3.4 - - - +
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Residues in contact with ALA 119 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G TRP* 3.4 36.7 - - + -
65G PHE* 3.5 29.5 - - + +
97G GLN* 2.8 23.6 + - + +
117G ASN* 3.8 2.2 - - - +
118G GLU* 1.3 77.7 - - - +
120G SER* 1.3 57.8 + - - +
122G LEU* 3.3 2.9 + - - +
123G HIS* 2.9 28.4 + - - +
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Residues in contact with SER 120 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G TRP* 4.1 10.9 + - - +
98G ARG 3.3 18.0 + - - -
100G ASN* 3.4 20.6 + - - -
113G LEU* 4.1 7.8 - - - +
115G CYS 3.4 19.2 + - - -
117G ASN* 2.6 29.3 + - - -
119G ALA* 1.3 70.6 - - - +
121G VAL* 1.3 66.2 + - - +
123G HIS* 3.2 6.2 + - - +
124G ASN* 2.9 25.0 + - - +
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Residues in contact with VAL 121 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G MET* 3.2 35.7 - - + +
113G LEU* 5.5 1.3 - - + -
116G LEU* 5.7 4.3 - - + -
117G ASN 3.0 22.1 + - - +
118G GLU* 3.6 8.5 - - - +
120G SER* 1.3 76.3 - - - +
122G LEU* 1.3 64.2 + - - +
124G ASN 3.0 2.6 + - - -
125G LEU* 2.9 35.8 + - + +
716G LEU* 4.0 21.3 - - + -
721G VAL* 4.9 10.8 - - + -
722G LEU* 5.6 0.4 - - + -
725G ILE* 3.9 28.5 - - + -
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Residues in contact with LEU 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G GLY* 4.9 0.2 - - - -
65G PHE* 4.5 16.6 - - + +
118G GLU 2.8 18.3 + - - +
119G ALA* 3.7 5.4 - - - +
121G VAL* 1.3 77.4 - - - +
123G HIS* 1.3 59.4 + - - +
125G LEU* 3.5 5.4 + - - +
126G ARG* 2.9 62.8 + - + +
707G LEU* 4.7 4.6 - - + +
709G PRO* 3.4 45.5 - - + +
712G VAL* 4.7 10.5 - - + -
713G LEU* 3.6 28.5 - - + +
716G LEU* 5.2 5.6 - - + -
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Residues in contact with HIS 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G TRP* 3.3 46.8 - + + -
99G MET* 4.8 12.9 - - + +
105G SER* 4.8 17.3 - - - -
106G LYS 5.6 0.2 + - - -
119G ALA 2.9 14.2 + - - +
120G SER* 3.6 6.1 - - - +
122G LEU* 1.3 78.4 - - - +
124G ASN* 1.3 64.8 + - + +
126G ARG* 3.3 20.5 + - - +
127G GLU* 2.8 59.5 + - - +
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Residues in contact with ASN 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104G PHE 5.3 0.9 - - - -
106G LYS* 3.3 28.3 + - - +
107G ALA* 3.5 28.9 + - - +
110G MET* 3.6 29.4 - - + +
113G LEU* 4.5 12.5 - - + +
120G SER 2.9 13.4 + - - +
121G VAL 3.0 6.5 + - - +
123G HIS* 1.3 86.2 - - + +
125G LEU* 1.3 57.3 + - - +
127G GLU* 3.2 5.2 + - - +
128G ARG* 2.9 31.6 + - - +
136G THR* 4.2 4.6 - - - +
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Residues in contact with LEU 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G MET* 3.9 12.8 - - + -
121G VAL* 2.9 33.9 + - + +
122G LEU* 3.9 4.3 - - - +
124G ASN* 1.3 77.0 - - - +
126G ARG* 1.3 56.6 + - - +
128G ARG* 3.2 6.3 + - - +
129G TYR* 2.9 30.6 + - - +
133G LEU 5.1 0.2 - - - +
136G THR* 3.6 37.9 - - + +
143G VAL* 4.3 25.8 - - + -
145G ILE* 4.3 19.9 - - + +
696G ILE* 5.6 0.9 - - + -
707G LEU* 4.5 3.5 - - + +
712G VAL* 4.8 9.6 - - + -
716G LEU* 4.6 17.9 - - + -
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Residues in contact with ARG 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G TRP* 3.7 34.1 - - - -
63G HIS* 4.0 30.8 + - - +
65G PHE 3.3 18.2 + - - -
66G GLU* 5.0 1.8 - - - +
122G LEU* 2.9 33.2 + - + +
123G HIS* 3.6 16.0 + - - +
125G LEU* 1.3 72.4 - - - +
127G GLU* 1.3 60.5 + - - +
129G TYR* 3.2 1.2 + - - +
130G TYR* 2.9 67.0 + - + -
707G LEU* 3.9 31.1 - - + +
709G PRO* 5.3 1.3 - - - +
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Residues in contact with GLU 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G SER* 5.4 4.2 - - - -
106G LYS* 3.4 30.9 - - + +
123G HIS* 2.8 44.8 + - + +
124G ASN* 3.3 9.0 - - - +
126G ARG* 1.3 78.0 - - - +
128G ARG* 1.3 60.7 + - - +
130G TYR* 3.4 6.0 + - - +
131G SER* 2.9 31.9 + - - -
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Residues in contact with ARG 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G LYS* 3.5 40.4 + - - +
107G ALA 2.4 35.5 + - - -
108G GLU* 3.6 6.2 + - - +
124G ASN* 2.9 30.2 + - - +
125G LEU* 3.2 6.9 + - - +
127G GLU* 1.3 76.7 - - - +
129G TYR* 1.4 56.9 + - - +
131G SER* 3.1 4.2 + - - -
132G GLY 3.0 5.0 + - - -
133G LEU* 2.7 67.1 + - - +
135G TYR 3.3 15.7 + - - -
136G THR* 3.3 33.7 + - - +
172G PRO* 3.6 21.0 - - - +
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Residues in contact with TYR 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G LEU 2.9 16.8 + - - +
126G ARG 3.6 3.8 - - - +
128G ARG* 1.4 76.0 - - - +
130G TYR* 1.3 68.5 + + - +
132G GLY* 2.9 18.9 + - - -
133G LEU 3.6 11.0 - - - +
134G ILE* 5.3 3.1 - - - -
145G ILE* 4.0 39.5 - - + -
146G ASN 4.5 0.2 - - - -
147G PRO* 3.7 17.3 - - + +
698G PRO* 3.6 19.3 - - + +
703G ARG 4.3 0.2 + - - -
704G ALA* 3.3 29.4 - - + +
705G GLY* 3.8 17.9 - - - -
706G LYS 3.9 17.0 + - - -
707G LEU* 3.9 27.1 - - + -
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Residues in contact with TYR 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63G HIS* 5.7 5.3 - + - -
126G ARG* 2.9 55.9 + - + +
127G GLU* 4.1 5.6 - - - +
129G TYR* 1.3 82.0 - + - +
131G SER* 1.3 59.9 + - - +
132G GLY* 3.0 2.0 + - - -
705G GLY* 3.7 33.4 + - - -
706G LYS* 4.1 4.6 - - - +
707G LEU* 3.1 33.3 + - + +
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Residues in contact with SER 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G LYS* 2.9 37.9 + - - +
127G GLU* 2.9 20.4 + - - -
128G ARG 3.1 6.0 + - - -
130G TYR* 1.3 77.0 - - - +
132G GLY* 1.3 58.0 + - - +
133G LEU* 4.4 8.4 - - - +
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Residues in contact with GLY 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129G TYR* 2.9 15.1 + - - -
130G TYR 3.0 2.7 - - - -
131G SER* 1.3 79.8 - - - +
133G LEU* 1.3 67.4 + - - +
134G ILE* 3.5 6.1 + - - +
151G LEU* 4.9 10.2 - - - +
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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