Contacts of the helix formed by residues 130 - 140 (chain A) in PDB entry 2GRQ
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 GLN 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A LEU 3.4 19.2 + - - -
82A PHE* 4.3 4.8 - - - +
83A HIS 3.0 26.1 + - - +
84A PRO 4.1 1.5 - - - +
86A VAL 2.9 22.4 + - - +
87A TYR 4.7 3.0 + - - -
88A PRO* 4.3 19.4 - - + +
128A PRO* 3.5 4.6 - - - +
129A ALA* 1.3 81.3 - - - +
131A ALA* 1.3 62.6 + - - +
132A GLU* 3.3 14.7 - - + +
133A ALA* 2.9 31.6 + - + +
134A TYR* 3.4 18.2 - - - +
514B THR* 6.5 0.2 - - - -
523B LEU* 4.6 4.3 - - - -
562B PHE* 4.6 3.4 - - - -
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Residues in contact with ALA 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A PRO* 6.0 0.2 - - - +
130A GLN* 1.3 72.1 - - - +
132A GLU* 1.3 59.2 + - - +
134A TYR* 3.5 1.0 + - - +
135A THR* 2.7 38.2 + - - -
513B LEU* 6.6 0.2 - - + -
514B THR* 4.5 15.7 + - - +
517B LEU* 4.5 12.8 - - + -
523B LEU* 4.5 6.9 - - + +
558B LEU* 4.2 20.0 - - + -
562B PHE* 3.5 27.5 - - + -
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Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A PHE* 3.9 18.1 - - + -
130A GLN* 3.3 11.6 - - + +
131A ALA* 1.3 79.8 - - - +
133A ALA* 1.3 64.4 + - - +
135A THR* 3.6 4.1 - - - -
136A ILE* 3.2 44.6 + - - +
147A ARG* 5.3 3.1 + - - -
510B ASN* 5.8 0.3 - - - +
558B LEU* 4.4 21.2 - - + +
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Residues in contact with ALA 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A PHE* 3.6 22.4 - - + -
83A HIS* 3.4 38.1 - - - +
84A PRO* 3.4 6.3 - - + -
130A GLN* 2.9 23.8 + - - +
131A ALA 3.6 0.2 - - - -
132A GLU* 1.3 74.2 - - - +
134A TYR* 1.3 57.8 + - - +
137A TYR* 2.9 32.2 + - - +
144A TYR* 3.9 3.5 - - + -
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Residues in contact with TYR 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A PRO* 4.3 7.9 - - + +
125A ILE* 3.1 44.2 + - + +
128A PRO* 3.6 24.0 - - + -
130A GLN 3.4 20.9 + - - +
131A ALA 3.5 2.0 + - - +
132A GLU 3.3 0.6 - - - -
133A ALA* 1.3 76.8 - - - +
135A THR* 1.3 67.6 + - - +
137A TYR* 3.3 4.9 + - - +
138A CYS* 3.0 42.4 + - + -
561B ALA* 3.9 28.2 + - + -
562B PHE* 3.7 19.3 - + + -
565B LYS* 3.3 36.2 - - + +
566B PRO* 5.5 0.7 - - - +
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Residues in contact with THR 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A ALA 2.7 23.2 + - - -
132A GLU* 3.3 4.5 + - - -
134A TYR* 1.3 81.9 - - - +
136A ILE* 1.3 60.8 + - + +
138A CYS* 3.8 1.5 - - - +
139A GLN* 2.9 58.9 + - - +
557B PRO* 3.6 19.1 - - + +
558B LEU* 3.5 20.7 - - + +
561B ALA* 3.5 17.6 - - + +
562B PHE* 4.2 2.3 - - - -
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Residues in contact with ILE 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A PHE* 3.8 11.9 - - + -
132A GLU* 3.2 36.1 + - - +
133A ALA 4.1 3.1 - - - +
135A THR* 1.3 76.2 - - + +
137A TYR* 1.3 67.2 + - - +
139A GLN* 4.8 2.7 - - - -
140A ASN* 2.8 34.2 + - + +
143A GLU* 4.0 9.2 - - + -
144A TYR* 3.7 28.7 - - - +
147A ARG* 3.1 43.1 - - - +
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Residues in contact with TYR 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A PRO* 4.4 2.7 - - + -
123A PRO* 3.9 20.2 - - + +
125A ILE* 3.3 38.8 - - + +
133A ALA 2.9 19.3 + - - +
134A TYR* 3.6 6.3 - - - +
136A ILE* 1.3 78.3 - - - +
138A CYS* 1.3 72.2 + - - +
141A ARG* 3.4 61.4 + - - +
144A TYR* 3.5 41.8 - + + -
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Residues in contact with CYS 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ILE* 3.9 16.2 - - - -
134A TYR* 3.0 58.1 + - + +
135A THR* 3.9 3.1 - - - +
137A TYR* 1.3 82.5 - - - +
139A GLN* 1.3 62.6 + - + +
141A ARG 5.4 0.2 - - - -
561B ALA* 5.7 2.5 - - + -
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Residues in contact with GLN 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A THR* 2.9 27.6 + - - +
136A ILE* 4.3 2.5 - - - +
138A CYS* 1.3 83.1 - - + +
140A ASN* 1.3 62.6 + - + +
557B PRO* 3.1 46.6 + - - +
560B LEU* 4.8 9.1 - - - +
561B ALA* 3.9 13.5 - - - +
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Residues in contact with ASN 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ILE* 2.8 20.5 + - + +
138A CYS 3.7 0.2 - - - -
139A GLN* 1.3 78.4 + - + +
141A ARG* 1.3 58.8 + - - +
142A VAL* 3.4 11.4 + - - +
143A GLU* 2.8 41.5 + - + +
144A TYR 2.9 23.7 + - - -
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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