Contacts of the helix formed by residues 136 - 145 (chain B) in PDB entry 1H3F
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 THR 136 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLU 4.4 14.1 - - - +
135A LEU 4.3 3.6 - - - -
136A THR* 5.6 0.2 - - - +
134B GLY 3.8 9.4 - - - +
135B LEU* 1.3 74.7 - - - +
137B PHE* 1.3 59.8 + - - +
138B LYS* 3.7 8.9 + - - +
139B GLU* 2.7 63.8 + - - +
140B VAL* 2.9 12.5 + - - +
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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
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79A PHE* 3.3 30.5 - + + -
132A LEU* 3.8 21.1 - - + +
133A GLU 4.8 1.4 + - - +
135A LEU* 3.3 42.7 + - + +
140A VAL* 3.6 28.7 - - + -
143A LEU* 6.4 0.4 - - + -
174A LEU* 4.4 26.5 - - + -
175A TYR* 5.5 2.5 - + - -
177A PHE* 5.7 1.6 - - + -
178A ALA* 3.8 29.2 - - + -
135B LEU 4.0 0.2 + - - -
136B THR* 1.3 72.1 - - - +
138B LYS* 1.3 55.4 + - - +
140B VAL* 3.3 9.8 + - + -
141B VAL* 3.0 40.0 + - + +
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Residues in contact with LYS 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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79A PHE* 4.0 25.8 - - + -
133A GLU* 5.7 6.8 + - + +
136B THR* 3.0 9.3 + - - +
137B PHE* 1.3 79.4 - - - +
139B GLU* 1.3 63.2 + - + +
141B VAL* 3.3 7.8 + - + +
142B ARG* 3.1 63.1 + - + +
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Residues in contact with GLU 139 (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 GLY 4.1 1.2 - - - +
135B LEU* 3.5 28.4 - - + +
136B THR* 2.7 50.9 + - - +
138B LYS* 1.3 76.2 - - + +
140B VAL* 1.3 61.1 + - - +
142B ARG* 3.3 17.1 + - - +
143B LEU* 2.9 33.6 + - - +
181B TYR* 4.9 4.7 + - - -
211B TYR* 4.3 8.6 + - - +
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PHE* 3.5 49.1 - - + -
140A VAL* 4.5 13.2 - - + -
174A LEU* 4.1 16.6 - - + -
135B LEU* 4.5 10.1 - - + -
136B THR 2.9 21.0 + - - +
137B PHE* 3.6 13.2 - - + +
139B GLU* 1.3 75.7 - - - +
141B VAL* 1.3 64.0 + - - +
143B LEU* 3.3 9.3 + - + +
144B THR* 3.0 31.4 + - + +
174B LEU* 4.7 3.1 - - + -
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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
----------------------------------------------------------
79A PHE* 4.9 4.9 - - + -
171A HIS* 3.5 18.9 - - + +
174A LEU* 4.3 8.1 - - + -
175A TYR* 3.8 31.2 - - + +
137B PHE* 3.0 44.1 + - + +
138B LYS* 3.4 11.0 - - + +
139B GLU 3.2 0.2 - - - -
140B VAL* 1.3 77.2 - - - +
142B ARG* 1.3 66.0 + - + +
144B THR* 3.3 8.8 + - - -
145B SER* 3.1 19.9 + - - -
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Residues in contact with ARG 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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138B LYS* 3.1 54.8 + - + +
139B GLU* 3.3 18.0 + - - +
141B VAL* 1.3 78.3 - - + +
143B LEU* 1.3 63.4 + - - +
145B SER* 2.7 24.7 + - - -
146B LEU* 3.7 9.8 - - - +
211B TYR* 5.0 7.2 - - + +
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Residues in contact with LEU 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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137A PHE* 6.0 2.9 - - + -
135B LEU* 4.1 26.5 - - + -
139B GLU 2.9 16.3 + - - +
140B VAL* 3.5 10.8 - - + +
141B VAL 3.2 0.2 - - - -
142B ARG* 1.3 77.3 - - - +
144B THR* 1.3 63.7 + - + +
146B LEU* 3.2 23.8 + - + +
177B PHE* 3.3 35.4 - - + +
178B ALA* 5.9 0.4 - - - -
181B TYR* 4.2 18.8 - - + -
207B VAL* 3.7 36.3 - - + -
211B TYR* 3.7 23.1 + - + +
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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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170A LEU* 3.1 31.7 - - + +
171A HIS* 3.2 30.5 + - - +
174A LEU* 3.4 10.6 - - + +
140B VAL* 3.0 21.2 + - + +
141B VAL 3.3 0.5 + - - -
143B LEU* 1.3 71.3 - - + +
145B SER* 1.3 59.6 + - - +
146B LEU 3.0 6.7 + - - -
147B MET 3.3 7.2 + - - +
174B LEU* 3.7 30.3 - - + -
177B PHE* 4.0 23.7 - - + -
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Residues in contact with SER 145 (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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169A SER* 3.2 18.7 + - - -
171A HIS* 3.4 24.5 - - - -
141B VAL* 3.1 12.3 + - - -
142B ARG* 2.7 23.2 + - - -
144B THR* 1.3 77.0 + - - +
146B LEU* 1.3 66.3 + - - +
147B MET 3.3 1.7 + - - +
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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