Contacts of the helix formed by residues 124 - 134 (chain G) in PDB entry 6R7H
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 124 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318D ASN 5.7 1.6 - - - +
319D ILE* 4.2 12.3 - - + +
320D THR* 6.1 0.4 - - - +
323D GLU* 4.1 25.7 - - + +
327D LEU* 5.2 3.2 - - - +
117G LEU* 3.5 15.6 - - - +
122G MET* 4.0 1.4 - - - +
123G ARG* 1.3 94.7 + - + +
125G LEU* 1.3 66.6 + - - +
126G ARG* 3.6 12.7 - - - +
127G GLU* 3.0 46.0 + - - +
128G LEU* 3.6 12.6 + - - +
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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
----------------------------------------------------------
317D ASN* 4.0 14.4 - - + -
318D ASN* 3.4 46.8 + - - +
113G TYR* 4.1 22.4 - - + -
117G LEU* 4.0 25.8 - - + -
124G ASN* 1.3 79.3 - - - +
126G ARG* 1.3 60.2 + - - +
127G GLU 3.4 0.4 - - - -
128G LEU* 3.3 6.0 + - + +
129G GLU* 2.9 45.9 + - - +
150G GLN* 3.8 18.6 - - - +
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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
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270D ASP 5.2 0.4 + - - -
271D ARG 4.6 4.4 + - - -
272D ILE* 3.5 33.6 - - - +
308D ASN* 5.0 10.3 + - - +
311D SER* 4.3 12.8 + - - -
312D ALA* 3.8 15.5 - - - +
315D LEU* 3.4 31.9 - - - +
316D TYR* 2.4 209.6 + - + -
317D ASN 5.1 1.2 - - - +
318D ASN 5.1 2.2 + - - -
319D ILE* 4.4 10.3 - - + +
327D LEU* 4.8 1.3 - - + -
124G ASN* 3.6 9.9 - - - +
125G LEU* 1.3 78.6 - - - +
127G GLU* 1.3 59.0 + - - +
129G GLU* 3.3 4.8 + - - +
130G ASP* 2.8 24.3 + - - -
133G ILE* 4.5 8.3 - - - +
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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
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316D TYR* 5.4 1.1 - - - -
323D GLU* 4.8 0.9 - - - +
327D LEU* 4.7 17.7 - - + +
122G MET* 3.3 36.3 - - + +
123G ARG* 4.2 24.8 + - - +
124G ASN* 3.0 33.9 + - - +
126G ARG* 1.3 77.9 - - - +
128G LEU* 1.3 62.0 + - - +
130G ASP* 3.4 19.6 + - + +
131G LEU* 4.3 4.0 + - + +
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Residues in contact with LEU 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G ILE* 5.7 1.6 - - + -
113G TYR* 4.1 11.4 - - + +
116G LEU* 3.4 52.3 - - + +
117G LEU* 3.8 22.4 - - + -
120G LEU* 3.8 26.4 - - + +
122G MET* 3.8 19.9 - - + +
124G ASN 3.6 16.7 + - - +
125G LEU* 3.3 13.6 + - + +
126G ARG 3.2 0.6 - - - -
127G GLU* 1.3 81.9 - - - +
129G GLU* 1.3 64.9 + - + +
130G ASP 3.2 0.7 + - - -
131G LEU* 4.0 6.4 + - - +
132G ILE* 4.0 12.0 - - + +
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Residues in contact with GLU 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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315D LEU 3.4 20.5 - - - +
316D TYR* 4.3 3.3 - - + -
317D ASN* 2.9 37.2 + - - +
113G TYR* 4.0 18.2 - - + -
125G LEU* 2.9 37.1 + - - +
126G ARG* 3.3 4.2 + - - +
128G LEU* 1.3 79.8 - - + +
130G ASP* 1.3 62.2 + - - +
131G LEU 3.3 1.3 - - - -
132G ILE* 3.2 18.8 + - + +
133G ILE* 3.2 28.8 + - + +
145G LEU* 3.8 20.2 - - + -
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Residues in contact with ASP 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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272D ILE* 4.0 23.3 - - - +
316D TYR* 3.2 29.5 + - + +
126G ARG* 2.8 16.6 + - - +
127G GLU* 3.5 17.5 - - + +
128G LEU 3.2 1.0 - - - -
129G GLU* 1.3 79.3 - - - +
131G LEU* 1.3 70.1 + - + +
133G ILE* 3.3 24.3 - - - +
134G GLU* 3.7 13.3 - - - +
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Residues in contact with LEU 131 (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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94G ASN* 4.0 30.1 - - + +
97G LYS* 3.8 40.4 - - + +
98G HIS* 3.1 49.5 + - + +
101G ILE* 6.1 1.1 - - + +
120G LEU* 5.0 5.2 - - + -
122G MET* 4.7 3.6 - - + -
127G GLU 4.6 9.6 - - - +
128G LEU 4.0 7.4 + - - +
129G GLU 3.3 0.4 - - - -
130G ASP* 1.3 89.1 - - + +
132G ILE* 1.3 63.7 + - + +
134G GLU* 4.1 11.6 + - + +
135G ALA* 4.4 1.7 + - - +
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Residues in contact with ILE 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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101G ILE* 3.9 38.6 - - + -
116G LEU* 4.6 5.6 - - + -
120G LEU* 6.0 0.4 - - + -
128G LEU* 4.0 17.5 - - + +
129G GLU* 3.2 21.4 + - + +
131G LEU* 1.3 79.8 - - + +
133G ILE* 1.3 67.7 + - + +
134G GLU 3.1 1.6 - - - -
135G ALA* 3.2 17.6 + - - +
136G VAL* 3.6 11.6 - - + +
141G ILE* 4.3 23.9 - - + +
145G LEU* 6.1 2.5 - - + -
152G LEU* 4.0 28.7 - - + -
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Residues in contact with ILE 133 (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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270D ASP 5.6 1.6 - - - +
272D ILE* 5.4 3.8 - - + -
315D LEU* 3.7 56.3 - - + +
316D TYR* 5.6 0.4 - - + -
126G ARG* 4.5 9.6 - - - +
129G GLU* 3.2 19.4 + - + +
130G ASP* 3.3 22.2 - - - +
132G ILE* 1.3 78.8 - - + +
134G GLU* 1.3 80.7 + - + +
135G ALA 3.2 0.4 - - - -
136G VAL* 3.3 24.5 + - + +
137G TYR* 3.5 23.2 - - + +
145G LEU* 5.1 9.4 - - + -
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Residues in contact with GLU 134 (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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271D ARG* 3.4 31.1 + - - +
272D ILE* 4.8 15.7 + - + +
98G HIS* 4.8 10.1 - - + +
130G ASP* 3.7 19.7 + - - +
131G LEU* 4.2 13.7 - - + +
132G ILE 3.1 1.2 - - - -
133G ILE* 1.3 97.5 - - + +
135G ALA* 1.3 57.7 + - - +
136G VAL 3.3 0.7 + - - -
137G TYR* 4.2 17.0 + - - -
138G THR* 3.3 15.8 + - - +
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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
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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