Contacts of the helix formed by residues 135 - 145 (chain A) in PDB entry 6FIT
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 MET 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.4 40.4 - - + -
26A VAL* 3.9 14.8 - - + +
27A ASN 4.2 3.1 - - - +
28A ARG* 3.4 34.5 - - + -
130A ARG* 3.6 45.3 - - + +
131A SER 2.7 12.2 + - - +
132A GLU* 4.3 18.8 - - - +
134A GLU* 1.3 75.7 - - - +
136A ALA* 1.3 63.2 + - - +
137A ALA 2.9 1.6 + - - -
138A GLU* 3.1 13.9 + - - +
139A ALA* 3.1 13.4 + - - +
148A AMW 4.2 8.1 - - + +
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Residues in contact with ALA 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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13A SER* 3.5 33.2 + - - +
132A GLU 3.8 15.8 + - - +
133A GLU* 3.8 8.8 + - - +
134A GLU 3.2 0.4 - - - -
135A MET* 1.3 78.9 - - - +
137A ALA* 1.3 59.3 + - - +
139A ALA* 3.7 6.0 - - - +
140A ALA* 3.2 23.0 + - - +
143A ARG* 4.4 2.3 + - - -
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Residues in contact with ALA 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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133A GLU 3.4 12.0 + - - +
134A GLU* 3.0 14.2 + - + +
135A MET 2.9 0.2 + - - -
136A ALA* 1.3 76.7 - - - +
138A GLU* 1.3 65.5 + - - +
139A ALA 2.7 5.1 + - - -
140A ALA* 3.0 5.9 + - - +
141A ALA* 2.9 23.5 + - - +
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Residues in contact with GLU 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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26A VAL* 3.3 19.8 - - + +
34A GLY* 4.1 11.6 + - - -
35A HIS 5.1 0.5 + - - +
36A VAL* 4.5 2.3 - - - +
72A HIS* 5.7 1.8 - - - +
73A PHE* 3.2 36.6 - - + -
130A ARG* 2.7 44.2 + - - +
134A GLU* 3.0 6.8 + - + +
135A MET 3.7 7.6 - - - +
137A ALA* 1.3 78.6 - - - +
139A ALA* 1.3 60.0 + - - +
141A ALA* 3.6 8.6 - - + +
142A LEU* 3.2 29.1 + - + +
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Residues in contact with ALA 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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14A VAL* 3.7 29.6 - - - +
16A PHE* 4.0 9.4 - - + +
26A VAL* 4.0 8.9 - - + +
135A MET 3.1 13.9 + - - +
136A ALA 3.7 3.8 - - - +
137A ALA 2.7 0.8 + - - -
138A GLU* 1.3 74.4 - - - +
140A ALA* 1.3 54.3 + - - +
141A ALA 2.9 1.6 - - - -
142A LEU* 2.7 8.1 + - - +
143A ARG* 2.7 53.1 + - - +
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Residues in contact with ALA 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 ALA 3.2 13.8 + - - +
137A ALA* 3.0 5.2 + - - +
139A ALA* 1.3 78.4 - - - +
141A ALA* 1.3 65.6 + - - +
143A ARG* 3.2 29.7 + - - +
144A VAL* 3.3 16.7 + - - +
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Residues in contact with ALA 141 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A HIS* 4.1 21.2 - - + +
137A ALA 2.9 16.5 + - - +
138A GLU* 3.6 11.0 - - - +
140A ALA* 1.3 79.5 - - - +
142A LEU* 1.3 61.6 + - - +
144A VAL* 3.3 20.1 - - - +
145A TYR* 3.8 10.3 - - - -
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A PHE* 3.6 46.0 - - + -
26A VAL* 4.4 1.8 - - + -
36A VAL* 4.1 14.1 - - + -
68A VAL* 4.1 19.5 - - + +
69A VAL* 4.1 5.2 - - + -
72A HIS* 4.1 18.2 - - + +
73A PHE* 3.9 21.5 - - + -
138A GLU* 3.2 24.2 + - + +
139A ALA 2.7 11.9 + - - +
141A ALA* 1.3 71.0 - - - +
143A ARG* 1.3 64.1 + - - +
144A VAL 2.7 6.4 + - - -
145A TYR* 2.9 23.1 + - + +
146A PHE* 3.7 9.7 - - + -
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Residues in contact with ARG 143 (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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12A PRO 4.5 5.5 + - - -
13A SER* 4.0 22.8 - - - +
14A VAL 4.1 1.2 - - - +
15A VAL 3.9 17.8 + - - -
16A PHE* 4.0 24.2 - - - +
136A ALA 4.4 2.2 + - - -
139A ALA* 2.7 23.5 + - - +
140A ALA* 3.4 40.0 - - - +
142A LEU* 1.3 72.5 - - - +
144A VAL* 1.3 61.6 + - + +
146A PHE* 3.3 15.0 + - + +
147A GLN* 3.7 12.8 + - - +
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Residues in contact with VAL 144 (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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140A ALA 3.3 15.0 + - - +
141A ALA* 3.3 12.8 - - - +
142A LEU 2.7 2.2 + - - -
143A ARG* 1.3 78.4 - - + +
145A TYR* 1.3 67.5 + - + +
147A GLN* 3.3 43.0 - - - +
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Residues in contact with TYR 145 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A VAL* 3.9 29.2 - - + +
71A LYS* 3.5 44.3 + - + +
72A HIS* 3.0 49.9 + + + +
141A ALA 3.8 11.7 - - - -
142A LEU* 2.9 20.4 + - - +
144A VAL* 1.3 82.2 - - + +
146A PHE* 1.3 63.1 + - + +
147A GLN 3.4 1.1 - - - +
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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
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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