Contacts of the helix formed by residues 135 - 144 (chain B) in PDB entry 4ZSQ
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 PRO 135 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B SER* 3.4 25.6 - - - +
38B PHE 6.0 0.4 - - - +
120B GLY 4.5 4.3 - - - +
121B LEU 5.8 0.4 - - - -
122B ALA 3.7 14.4 - - - +
123B TYR 3.9 0.9 - - - -
124B ALA* 3.5 38.8 - - + +
127B ALA* 4.8 0.4 - - + -
133B LEU 3.5 6.1 - - - +
134B GLU* 1.4 88.8 - - + +
136B PHE* 1.3 68.2 + - - +
137B PHE* 3.3 3.4 - - + +
138B ASP* 3.2 29.6 + - - +
139B SER* 3.2 16.6 + - - -
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Residues in contact with PHE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B MET* 4.0 10.1 - - + -
36B SER 4.8 0.6 + - - -
38B PHE* 4.3 20.5 - + + +
85B VAL* 3.5 28.9 - - + -
86B SER* 6.1 0.2 - - - -
87B ILE* 4.1 24.5 - - + -
95B VAL* 3.8 22.2 - - + -
97B ALA* 3.8 20.9 - - + -
98B ASN 5.9 1.7 + - - +
119B LEU* 3.7 36.8 - - + -
120B GLY 4.7 6.5 + - - +
121B LEU* 5.0 2.7 - - + -
134B GLU 3.8 0.8 + - - -
135B PRO* 1.3 71.4 - - - +
137B PHE* 1.3 71.1 + + + +
139B SER* 3.0 10.6 + - - -
140B LEU* 2.9 40.8 + - + -
176B ILE* 5.9 1.1 - - + -
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Residues in contact with PHE 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 4.2 28.0 - - + +
135B PRO* 3.3 3.9 + - + +
136B PHE* 1.3 83.7 - + - +
138B ASP* 1.3 58.0 + - - +
140B LEU* 3.1 15.0 + - + +
141B VAL* 2.9 40.1 + - + +
146B VAL* 4.8 0.4 - - + -
147B PRO 4.1 5.4 - - - -
148B ASN* 3.4 19.3 - - - -
149B LEU 3.5 31.9 - - - -
150B PHE* 3.9 23.3 - + + -
176B ILE* 3.9 30.5 - - + -
347B ARG* 3.4 33.4 - - - +
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Residues in contact with ASP 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ALA 4.8 1.2 - - - +
123B TYR* 5.1 4.7 - - - -
124B ALA* 4.9 5.3 + - - +
134B GLU* 3.7 18.8 - - + +
135B PRO* 3.2 35.2 + - - +
137B PHE* 1.3 74.7 - - - +
139B SER* 1.3 58.4 + - - +
141B VAL* 3.1 6.3 + - - +
142B LYS* 2.8 34.6 + - + +
347B ARG* 3.2 24.9 + - - +
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Residues in contact with SER 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B VAL* 4.7 2.5 - - - -
96B ARG 3.9 12.5 + - - -
97B ALA* 4.3 15.1 - - - +
98B ASN* 5.0 1.7 + - - -
134B GLU* 2.5 31.1 + - - +
135B PRO 3.2 7.7 + - - -
136B PHE* 3.0 10.6 + - - -
138B ASP* 1.3 79.3 - - - +
140B LEU* 1.3 57.2 + - - +
142B LYS* 4.5 1.8 - - - -
143B GLN* 2.9 50.4 + - - +
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ILE* 5.4 3.4 - - + -
91B PRO* 5.1 3.4 - - + -
93B VAL* 3.6 31.0 - - + -
95B VAL* 4.0 20.8 - - + +
136B PHE* 2.9 32.3 + - + +
137B PHE* 3.1 27.8 + - + +
139B SER* 1.3 75.1 - - - +
141B VAL* 1.3 55.1 + - + +
144B THR* 2.6 44.2 + - + +
146B VAL* 4.4 9.2 - - + -
176B ILE* 3.5 33.0 - - + -
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Residues in contact with VAL 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B PHE* 2.9 46.9 + - + +
138B ASP* 3.1 5.8 + - - +
140B LEU* 1.3 78.1 - - + +
142B LYS* 1.3 65.8 + - - +
144B THR 3.1 18.5 - - - +
146B VAL* 4.1 18.4 - - + +
147B PRO 4.4 0.9 - - - +
148B ASN* 3.8 32.8 - - + +
347B ARG* 6.1 0.2 - - - +
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Residues in contact with LYS 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B GLU* 3.5 24.1 + - - +
138B ASP* 2.8 21.1 + - + +
139B SER* 3.9 5.2 - - - +
141B VAL* 1.3 77.2 - - - +
143B GLN* 1.3 64.5 + - + +
144B THR 3.7 1.2 + - - +
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Residues in contact with GLN 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316A GLN* 4.8 3.9 + - - +
95B VAL* 3.3 17.6 - - + +
96B ARG* 2.8 50.0 + - - +
134B GLU* 4.7 3.6 + - - -
139B SER* 2.9 31.1 + - - +
142B LYS* 1.3 81.3 - - + +
144B THR* 1.3 60.1 + - - +
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Residues in contact with THR 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B VAL* 3.8 31.4 - - + -
94B THR 5.3 1.1 - - - +
95B VAL* 3.6 22.0 - - + -
140B LEU* 2.6 23.5 + - + +
141B VAL 3.1 14.4 - - - +
142B LYS 4.5 1.2 - - - +
143B GLN* 1.3 84.1 - - - +
145B HIS* 1.3 67.7 + - - +
146B VAL* 2.9 28.2 + - - +
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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