Contacts of the helix formed by residues 135 - 147 (chain d) in PDB entry 5GJQ
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 GLY 135 (chain d).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1d MET* 4.7 0.8 - - - +
3d TYR* 3.8 13.2 - - - +
133d GLY* 3.2 1.8 - - - -
134d TYR* 1.3 79.7 - - - +
136d ALA* 1.3 57.4 + - - +
138d LEU* 2.9 23.9 + - - +
139d THR* 3.0 17.1 + - - +
167d LEU* 3.7 22.4 - - - -
171d PHE* 3.8 13.7 - - - -
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Residues in contact with ALA 136 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33c GLN* 4.3 13.7 - - - +
3d TYR* 3.7 4.8 - - - -
131d ALA* 3.7 37.2 - - + +
132d HIS* 4.2 0.9 - - - +
133d GLY 3.1 17.1 + - - +
134d TYR 3.1 0.4 - - - -
135d GLY* 1.3 74.6 - - - +
137d PHE* 1.3 62.1 + - - +
139d THR* 3.0 9.0 + - - -
140d LEU* 2.9 36.1 + - + +
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Residues in contact with PHE 137 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32c ALA* 5.9 5.4 - - + -
33c GLN* 3.6 22.8 - - + +
133d GLY 4.0 5.6 - - - -
134d TYR* 3.1 47.7 + + + +
136d ALA* 1.3 78.2 - - - +
138d LEU* 1.3 59.4 + - + +
140d LEU 4.9 0.4 - - - -
141d SER* 4.8 0.3 + - - -
25r ILE* 4.9 6.5 - - + -
133s VAL* 3.3 39.4 - - + +
134s TYR* 3.3 55.1 - + - -
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Residues in contact with LEU 138 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134d TYR 4.5 5.6 - - - +
135d GLY* 2.9 10.5 + - - +
137d PHE* 1.3 77.0 - - + +
139d THR* 1.3 60.0 + - - +
141d SER* 3.8 11.9 + - - -
142d ILE* 4.0 2.3 - - - +
166d GLU* 3.7 27.7 - - + +
167d LEU* 4.2 17.7 - - + -
170d ARG* 4.1 13.5 - - + -
171d PHE* 4.0 37.5 - - + +
25r ILE* 5.1 2.2 - - + -
26r VAL* 4.3 12.8 - - + -
133s VAL* 3.6 42.2 - - + +
136s TYR* 4.7 10.1 - - + -
137s GLY* 4.0 7.1 - - - -
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Residues in contact with THR 139 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3d TYR* 3.0 28.7 + - + +
5d ILE* 4.9 1.8 - - - -
131d ALA* 4.3 3.5 - - - +
135d GLY 3.0 17.8 + - - +
136d ALA* 3.2 10.7 + - - -
138d LEU* 1.3 83.1 - - + +
140d LEU* 1.3 69.0 + - - +
141d SER 3.3 2.0 - - - -
142d ILE* 2.9 19.2 + - - +
143d LEU* 3.1 15.6 + - - +
163d CYS* 3.8 36.7 - - + +
166d GLU* 5.0 1.6 - - + -
167d LEU* 4.0 15.3 - - + -
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Residues in contact with LEU 140 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33c GLN* 3.6 34.3 - - - +
34c MET 4.5 0.2 - - - +
35c VAL* 6.0 1.1 - - + -
129d PHE* 4.0 6.1 - - + +
130d ALA* 4.3 9.2 - - + -
131d ALA* 4.0 33.9 - - + +
136d ALA* 2.9 18.6 + - + +
139d THR* 1.3 75.4 + - - +
141d SER* 1.3 59.3 + - - +
143d LEU* 3.0 12.9 + - + +
144d ASP* 2.7 31.8 + - - -
134s TYR* 4.5 2.9 - - + -
166s ARG* 3.1 49.8 - - + +
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Residues in contact with SER 141 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138d LEU 3.8 16.6 + - - -
140d LEU* 1.3 77.4 - - - +
142d ILE* 1.3 63.5 + - - -
144d ASP* 3.0 14.5 + - - +
145d ARG* 2.8 29.7 + - - +
134s TYR* 3.2 44.3 + - - -
137s GLY* 3.8 6.2 - - - -
138s VAL* 4.7 4.9 - - - -
162s GLN* 4.4 15.6 + - - +
166s ARG* 4.9 2.2 - - - +
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Residues in contact with ILE 142 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138d LEU 4.0 5.8 - - - +
139d THR 2.9 11.6 + - - +
141d SER* 1.3 78.4 + - - +
143d LEU* 1.3 63.8 + - - +
145d ARG* 3.0 9.8 + - - +
146d TYR* 2.9 34.2 + - + +
159d LEU* 4.0 13.2 - - + -
162d LYS* 4.2 15.0 - - + +
163d CYS* 3.8 20.0 - - - -
166d GLU* 3.6 36.1 - - + -
137s GLY* 3.6 33.2 - - - +
138s VAL* 5.1 1.1 - - - +
141s ARG* 3.8 13.2 - - + -
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Residues in contact with LEU 143 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5d ILE* 3.9 24.2 - - + -
7d ILE* 4.0 15.9 - - + -
129d PHE* 3.5 40.6 - - + -
130d ALA 5.0 1.8 - - - +
131d ALA* 5.6 0.2 - - + -
139d THR* 3.1 12.5 + - - +
140d LEU* 3.0 17.6 + - + +
142d ILE* 1.3 75.6 - - - +
144d ASP* 1.3 59.2 + - - +
146d TYR 3.0 0.3 + - - -
147d TYR* 2.7 38.7 + - + +
159d LEU* 3.6 26.7 - - + -
163d CYS* 3.6 20.6 - - - -
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Residues in contact with ASP 144 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129d PHE* 3.0 24.5 - - - -
140d LEU 2.7 16.9 + - - +
141d SER* 3.0 8.5 + - - +
143d LEU* 1.3 71.9 - - - +
145d ARG* 1.3 61.6 + - - +
147d TYR* 4.5 6.6 - - - +
158s ARG* 4.8 2.3 + - - -
162s GLN* 3.1 29.4 + - - +
165s TYR* 3.6 23.0 - - - -
166s ARG* 3.1 31.4 + - - +
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Residues in contact with ARG 145 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141d SER 2.8 12.0 + - - +
142d ILE* 3.0 13.0 + - - +
144d ASP* 1.3 80.6 - - - +
146d TYR* 1.3 98.8 + - + +
147d TYR 5.0 1.6 - - - +
138s VAL* 5.1 17.6 - - + +
158s ARG* 3.5 53.8 + - - +
162s GLN* 4.5 5.1 - - - +
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Residues in contact with TYR 146 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142d ILE* 2.9 27.5 + - + -
145d ARG* 1.3 121.9 + - + +
147d TYR* 1.3 62.6 + - - +
148d THR* 3.7 7.8 + - - +
151d ILE* 4.3 7.4 - - - +
159d LEU* 3.6 24.7 - - + +
162d LYS* 4.0 41.7 - - + +
138s VAL* 5.4 1.0 + - - -
141s ARG* 4.1 29.1 + - + +
142s GLY* 5.1 2.4 + - - -
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Residues in contact with TYR 147 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7d ILE* 3.8 26.0 - - + -
8d GLN* 2.6 31.2 + - - +
9d GLY 5.3 0.2 - - - -
128d PRO* 3.7 31.5 - - + +
129d PHE* 3.6 23.3 - + + -
143d LEU* 2.7 27.1 + - + +
144d ASP* 4.5 7.2 - - - +
145d ARG 5.0 0.7 - - - +
146d TYR* 1.3 73.5 - - - +
148d THR* 1.3 79.8 + - - +
149d PRO* 3.9 26.4 + - + +
151d ILE* 3.9 9.9 - - + -
159d LEU* 4.1 11.6 - - + +
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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