Contacts of the helix formed by residues 117 - 128 (chain A) in PDB entry 1L7R
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 SER 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A PHE* 6.0 2.2 - - - -
116A VAL* 1.3 82.2 - - - +
118A TYR* 1.3 66.9 + - - +
120A GLY* 2.8 17.3 + - - -
121A VAL* 3.0 17.9 + - - +
140A SER 2.9 12.5 + - - -
141A MET 3.5 14.8 - - - -
142A ALA* 4.0 2.8 - - - +
261A PHE* 4.5 10.1 - - - -
287A HIS* 2.9 30.3 + - - -
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Residues in contact with TYR 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PRO* 3.6 43.3 - - + -
44A PHE* 4.9 8.5 - - + -
74A THR* 4.5 5.2 - - + +
84A PHE* 4.4 9.5 - + - -
85A VAL 5.1 0.2 + - - -
86A PRO* 4.1 4.7 - - - +
87A HIS* 3.4 36.2 + + - -
90A ASP* 3.2 23.0 + - - -
117A SER* 1.3 84.0 + - - +
119A LEU* 1.3 62.0 + - - +
120A GLY 3.0 1.1 + - - -
121A VAL* 4.0 10.7 - - + +
122A THR* 3.1 40.9 + - + -
125A GLN* 5.4 0.2 - - - -
166A TRP* 3.5 39.3 - + - +
170A ILE* 5.1 0.9 - - + -
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Residues in contact with LEU 119 (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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40A VAL* 3.4 12.6 - - + -
41A ARG 2.8 32.4 + - - +
42A ASN* 3.2 30.5 - - + +
43A PRO* 4.5 1.6 - - + -
52A TRP* 3.3 56.5 - - + -
114A PHE 4.2 1.7 - - - +
115A GLY* 3.6 5.3 - - - -
116A VAL 2.8 24.5 + - - +
118A TYR* 1.3 77.0 - - + +
120A GLY* 1.3 56.5 + - - +
122A THR* 3.3 14.2 + - - -
123A GLN* 2.8 22.3 + - - +
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Residues in contact with GLY 120 (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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115A GLY 3.8 7.6 - - - -
116A VAL 3.7 1.8 + - - -
117A SER 2.8 11.8 + - - -
119A LEU* 1.3 79.8 - - - +
121A VAL* 1.3 63.1 + - - -
122A THR 3.2 1.6 - - - -
123A GLN* 3.0 31.1 + - - +
124A TRP* 3.7 4.3 + - - -
139A PRO* 3.7 10.1 - - - +
140A SER 4.3 1.3 - - - -
142A ALA* 3.4 16.1 - - - +
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A HIS* 4.7 9.4 - - + +
117A SER 3.0 14.0 + - - +
118A TYR* 3.4 12.1 + - + +
120A GLY* 1.3 75.2 - - - +
122A THR* 1.3 64.4 + - + +
123A GLN 3.2 0.9 + - - -
124A TRP* 3.2 13.8 + - - +
125A GLN* 3.4 25.5 + - + +
142A ALA* 3.5 2.7 - - + +
143A SER 3.7 36.8 - - - +
146A LEU* 4.0 29.6 - - + -
240A LEU* 5.5 1.3 - - + -
261A PHE* 4.4 14.6 - - + -
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Residues in contact with THR 122 (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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41A ARG* 3.7 44.6 + - - +
74A THR* 5.2 0.7 - - + -
90A ASP* 4.2 1.5 - - - +
94A ALA* 4.8 3.1 - - - +
113A MET* 4.3 3.8 - - - +
118A TYR* 3.1 45.9 + - + +
119A LEU 3.3 12.3 + - - -
121A VAL* 1.3 76.6 - - + +
123A GLN* 1.3 59.3 + - - +
125A GLN* 3.3 20.8 + - - +
126A ALA* 3.0 26.9 + - - +
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Residues in contact with GLN 123 (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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113A MET* 3.2 32.9 - - + +
114A PHE 3.1 29.4 - - - +
115A GLY 3.2 9.5 + - - +
119A LEU 2.8 25.0 + - - +
120A GLY* 3.0 11.3 + - - +
122A THR* 1.3 76.7 - - - +
124A TRP* 1.3 60.5 + - - +
126A ALA* 3.2 2.4 + - - +
127A ALA* 2.8 29.3 + - - +
137A ILE* 3.5 12.7 - - + +
138A ALA 2.8 40.9 + - - -
139A PRO* 3.4 9.6 - - + +
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Residues in contact with TRP 124 (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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120A GLY 3.7 13.6 + - - -
121A VAL 3.2 7.0 + - - +
123A GLN* 1.3 76.9 - - - +
125A GLN* 1.3 62.6 + - - +
127A ALA* 3.2 8.2 + - + +
128A VAL* 3.1 29.1 + - - +
137A ILE* 3.6 20.9 - - + -
139A PRO* 3.6 26.5 - - + +
142A ALA* 4.5 5.4 - - + +
143A SER 3.7 24.1 - - - +
144A ALA* 4.1 8.5 - - + -
240A LEU* 4.2 15.0 - - + -
244A LEU* 3.9 28.3 - - + -
247A LEU* 4.7 7.2 - - + -
249A THR* 5.8 2.7 - - - -
251A ALA* 3.9 15.3 - - + -
253A ILE* 4.0 9.6 - - + -
268A THR* 3.4 36.5 + - - +
272A VAL* 4.0 20.0 - - + -
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Residues in contact with GLN 125 (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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87A HIS* 3.1 40.0 + - - +
90A ASP* 3.1 25.5 - - - +
91A GLU* 3.6 38.0 + - + +
94A ALA* 4.8 0.2 - - - -
118A TYR* 5.4 0.2 - - - -
121A VAL* 3.5 18.7 - - - +
122A THR* 3.3 24.1 + - - +
123A GLN 3.2 0.4 - - - -
124A TRP* 1.3 78.3 - - - +
126A ALA* 1.3 56.7 + - - +
128A VAL* 3.1 24.1 - - - +
129A SER* 4.1 3.3 + - - -
146A LEU* 5.5 1.2 - - - +
238A ILE* 5.0 8.7 + - - +
240A LEU* 4.0 19.0 - - + +
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Residues in contact with ALA 126 (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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94A ALA* 3.6 24.2 - - + +
98A LEU* 4.1 10.5 - - + +
113A MET* 3.5 33.0 - - + -
122A THR 3.0 12.5 + - - +
123A GLN 3.6 0.7 - - - +
124A TRP 3.2 0.2 - - - -
125A GLN* 1.3 78.0 - - - +
127A ALA* 1.3 59.8 + - - +
129A SER* 2.6 29.0 + - - +
134A LEU* 3.8 8.5 - - + +
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Residues in contact with ALA 127 (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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123A GLN 2.8 17.1 + - - +
124A TRP* 3.2 11.6 + - + +
126A ALA* 1.3 78.3 - - - +
128A VAL* 1.3 60.0 + - - +
129A SER 3.1 9.9 - - - +
134A LEU* 3.8 15.5 - - + +
137A ILE* 4.2 17.3 - - + -
247A LEU* 3.5 29.1 - - + +
249A THR* 4.7 13.3 + - + +
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Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLU* 3.7 8.7 - - - +
124A TRP 3.1 14.1 + - - +
125A GLN 3.1 22.9 - - - +
127A ALA* 1.3 72.3 - - - +
129A SER* 1.3 64.7 + - - +
130A GLY 3.9 0.2 + - - -
240A LEU* 3.9 23.3 - - + +
243A ARG* 3.6 56.2 + - + +
244A LEU* 4.4 2.0 - - + -
247A LEU* 4.1 21.4 - - + +
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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