Contacts of the helix formed by residues 136 - 148 (chain T) in PDB entry 2P8W
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 CYS 136 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27T HIS* 3.3 27.1 - - + +
30T HIS* 4.0 6.5 - - - -
133T GLU* 3.9 34.5 - - - -
134T GLY 3.5 13.8 + - - -
135T VAL* 1.3 77.7 - - - +
137T VAL* 1.3 58.7 + - + +
138T GLN 3.2 0.4 - - - -
139T THR* 2.8 28.4 + - - +
140T GLU* 3.0 11.3 + - - +
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Residues in contact with VAL 137 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27T HIS* 5.1 4.9 - - - +
136T CYS* 1.3 73.0 - - + +
138T GLN* 1.3 64.0 + - + +
140T GLU* 3.2 14.6 + - - +
141T THR* 2.8 36.1 + - - +
482T LYS 5.9 3.1 - - - +
483T PHE* 5.5 11.2 - - + -
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Residues in contact with GLN 138 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26T ALA 4.5 1.8 - - - +
27T HIS* 2.9 33.4 + - + +
28T VAL* 2.8 52.5 + - - +
107T GLY 5.2 1.9 - - - +
109T VAL* 3.0 34.1 - - + +
136T CYS 3.1 0.6 + - - -
137T VAL* 1.3 83.4 - - + +
139T THR* 1.3 61.2 + - - +
141T THR* 3.3 7.3 + - - -
142T VAL* 3.2 28.9 + - - +
483T PHE* 5.5 4.0 - - + -
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Residues in contact with THR 139 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25T ILE* 4.2 9.9 - - + +
27T HIS* 3.4 27.6 + - - +
30T HIS* 4.4 5.4 + - - -
127T VAL* 4.1 25.8 - - + -
128T VAL 4.2 10.5 + - - +
129T VAL* 4.6 6.7 - - + -
135T VAL* 3.8 19.9 - - + -
136T CYS 2.8 18.4 + - - -
138T GLN* 1.3 76.8 - - - +
140T GLU* 1.3 64.2 + - - -
142T VAL* 3.5 0.5 + - - -
143T LEU* 3.1 29.3 + - + +
185T VAL* 6.3 0.4 - - + -
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Residues in contact with GLU 140 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135T VAL* 4.3 2.7 - - + +
136T CYS 3.0 9.7 + - - +
137T VAL* 3.6 17.2 - - - +
139T THR* 1.3 76.4 - - - +
141T THR* 1.3 51.6 + - - +
143T LEU* 3.9 1.9 - - - +
144T ARG* 2.8 15.2 + - - +
188T ILE* 3.4 44.2 - - + +
192T TYR* 4.8 8.4 + - + -
481T MET* 2.7 28.5 - - + +
482T LYS* 3.9 29.5 + - - +
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Residues in contact with THR 141 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109T VAL* 4.0 23.1 - - + +
111T PHE* 3.8 33.7 - - + +
137T VAL* 2.8 23.4 + - - +
138T GLN* 3.5 8.7 - - - -
139T THR 3.2 0.2 - - - -
140T GLU* 1.3 77.4 - - - +
142T VAL* 1.3 57.9 + - - +
145T GLN* 3.1 15.0 + - - +
481T MET* 2.6 41.0 - - - +
482T LYS 5.8 1.6 - - - -
483T PHE* 4.0 11.5 - - + -
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Residues in contact with VAL 142 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25T ILE* 3.5 39.0 - - + -
26T ALA 5.7 4.9 - - - +
105T SER* 5.9 3.6 - - - +
109T VAL* 2.9 37.5 - - + -
115T VAL* 4.4 8.3 - - + -
119T LEU* 4.1 17.6 - - + +
138T GLN 3.2 10.0 + - - +
141T THR* 1.3 73.5 - - - +
143T LEU* 1.3 55.9 + - - +
145T GLN* 3.2 10.0 + - - +
146T ALA* 2.7 33.3 + - - +
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Residues in contact with LEU 143 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25T ILE* 4.0 11.8 - - + +
125T ALA* 6.3 0.2 - - + -
127T VAL* 4.3 20.2 - - + -
135T VAL* 6.0 0.7 - - + -
139T THR* 3.1 21.6 + - + +
140T GLU 3.9 2.7 - - - +
142T VAL* 1.3 78.4 - - - +
144T ARG* 1.3 57.6 + - - +
146T ALA* 3.1 8.2 + - + +
147T LEU* 2.8 50.0 + - + +
153T PRO* 4.1 26.0 - - + -
185T VAL* 4.3 22.0 - - + -
188T ILE* 3.8 35.7 - - + -
189T VAL* 4.5 4.0 - - + -
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Residues in contact with ARG 144 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111T PHE* 3.7 3.8 - - - -
140T GLU* 2.8 6.8 + - - +
143T LEU* 1.3 74.8 - - - +
145T GLN* 1.3 59.0 + - - -
147T LEU* 3.4 11.4 + - - +
148T GLY* 3.1 17.7 + - - -
188T ILE* 4.6 2.6 - - + +
192T TYR* 2.9 56.2 + - + +
481T MET* 1.1 138.9 + - + +
482T LYS* 1.6 52.2 - - - +
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Residues in contact with GLN 145 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109T VAL* 5.2 0.9 - - - +
111T PHE* 3.4 30.4 + - + +
112T SER 3.0 27.1 + - - +
115T VAL* 3.9 20.6 - - - +
116T THR* 3.2 15.1 + - - +
119T LEU* 4.0 11.7 - - + -
141T THR* 3.1 18.8 + - - +
142T VAL* 3.5 9.1 - - - +
144T ARG* 1.3 67.0 - - - +
146T ALA* 1.3 64.3 + - - +
148T GLY* 3.1 10.6 + - - -
149T GLU* 3.3 15.9 + - - +
480T VAL 4.4 1.0 + - - -
481T MET* 1.7 74.8 + - + +
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Residues in contact with ALA 146 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25T ILE* 3.8 20.4 - - + -
119T LEU* 3.8 7.8 - - + +
125T ALA* 5.1 0.7 - - + -
142T VAL 2.7 18.7 + - - +
143T LEU* 3.3 12.6 - - + +
145T GLN* 1.3 73.8 - - - +
147T LEU* 1.3 54.5 + - + +
149T GLU* 2.7 25.1 + - - +
151T ILE* 3.3 46.9 + - + +
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Residues in contact with LEU 147 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143T LEU* 2.8 41.9 + - + +
144T ARG 3.7 4.5 - - - +
146T ALA* 1.3 71.6 - - + +
148T GLY* 1.3 57.4 + - - +
150T ARG* 2.9 19.2 + - - +
151T ILE 3.7 19.7 - - - +
153T PRO* 4.2 17.0 - - + -
188T ILE* 3.7 14.1 - - + +
189T VAL* 3.6 31.6 - - + +
192T TYR* 4.0 26.4 - - + +
193T ALA* 4.4 17.2 - - + +
194T ASP* 4.4 10.9 + - - +
197T LEU* 5.7 1.4 - - + +
200T VAL* 4.8 2.2 - - + -
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Residues in contact with GLY 148 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144T ARG 3.1 9.9 + - - -
145T GLN* 3.1 10.8 + - - -
146T ALA 3.0 1.6 - - - -
147T LEU* 1.3 76.4 - - - +
149T GLU* 1.3 64.6 + - - +
150T ARG* 3.2 3.1 + - - +
192T TYR* 5.1 3.1 + - - +
194T ASP* 5.5 3.8 - - - +
355T GLN* 4.4 13.5 + - - +
479T LYS* 5.5 3.8 + - - -
480T VAL 6.1 0.2 - - - -
481T MET* 5.0 7.4 - - - -
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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