Contacts of the helix formed by residues 117 - 130 (chain A) in PDB entry 4L1O
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 PHE 117 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A LEU* 6.4 0.2 - - + -
35A LEU* 4.3 9.9 - - + -
36A ILE* 3.6 30.5 - - + -
43A LEU* 3.7 31.4 - - + -
47A LEU* 5.1 0.4 - - + -
62A GLU* 2.7 18.8 + - - +
63A VAL* 4.0 26.0 - - + -
66A VAL* 3.7 33.9 - - + -
116A PRO* 1.3 74.9 - - - +
118A ASN* 1.3 59.9 + - - +
120A THR* 3.0 1.2 + - - -
121A ILE* 2.8 62.3 + - + +
145A MET* 4.0 14.8 - - + -
149A LEU* 4.1 14.8 - - + -
153A ILE* 6.3 0.4 - - + -
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Residues in contact with ASN 118 (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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62A GLU* 3.0 40.4 + - + +
65A TYR* 3.8 10.0 - - - +
66A VAL* 3.8 10.9 - - - +
115A TYR* 4.0 7.9 - - + +
117A PHE* 1.3 77.7 - - - +
119A LEU* 1.3 77.4 + - - +
120A THR 3.2 0.9 + - - -
122A GLN* 2.8 55.8 + - - +
123A PRO* 3.2 1.6 - - - +
412A TYR* 4.9 1.2 + - - -
601A 1VL 3.5 24.8 - - - -
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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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109A VAL* 4.2 3.5 - - - +
110A ILE 4.7 1.0 - - - +
111A GLY* 3.7 13.6 - - - -
112A THR* 3.3 35.9 - - + +
114A ASN* 3.4 11.2 - - - +
115A TYR* 2.8 33.4 + - + +
118A ASN* 1.3 85.4 - - - +
120A THR* 1.3 59.8 + - - +
123A PRO* 3.8 14.6 - - - +
184A LEU* 5.4 0.3 - - - +
186A THR* 4.4 14.8 + - + +
412A TYR* 3.8 8.5 - - - +
601A 1VL 3.3 54.7 - - + +
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Residues in contact with THR 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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109A VAL* 3.7 5.8 - - - +
111A GLY* 3.7 24.7 - - - +
112A THR 4.8 3.4 - - - +
116A PRO* 2.6 28.1 + - + +
117A PHE 3.0 5.2 + - - -
119A LEU* 1.3 78.6 - - - +
121A ILE* 1.3 81.4 + - - +
122A GLN 3.6 0.2 - - - -
123A PRO* 3.6 2.9 - - - +
124A MET* 3.5 19.4 + - - +
136A LEU* 3.7 23.7 - - + +
138A PRO* 4.3 19.3 - - + -
149A LEU* 3.6 12.6 - - + +
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Residues in contact with ILE 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.2 19.7 - - + -
36A ILE* 5.6 0.9 - - + -
66A VAL* 3.8 20.9 - - + -
117A PHE* 2.8 49.5 + - + +
120A THR* 1.3 89.7 + - - +
122A GLN* 1.3 57.7 + - - +
124A MET* 3.1 10.6 + - + +
125A VAL* 2.8 34.8 + - + +
136A LEU* 4.1 14.4 - - + -
149A LEU* 4.2 5.8 - - + -
153A ILE* 3.9 27.1 - - + -
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Residues in contact with GLN 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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65A TYR* 3.8 25.2 + - - +
66A VAL* 4.0 11.5 + - + +
69A GLU* 3.4 36.9 + - + +
117A PHE 4.1 0.2 + - - -
118A ASN* 2.8 54.5 + - - +
121A ILE* 1.3 73.7 - - - +
123A PRO* 1.3 62.0 - - + +
125A VAL* 3.4 14.0 + - - +
126A GLY* 3.5 8.8 + - - -
412A TYR* 4.6 3.5 - - + -
413A HIS* 3.4 40.2 + - + +
417A SER* 5.1 0.7 + - - -
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Residues in contact with PRO 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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109A VAL* 3.9 21.5 - - + -
118A ASN 3.2 12.8 - - - +
119A LEU* 3.8 16.8 - - - +
120A THR 3.6 8.7 - - - +
122A GLN* 1.3 91.8 - - + +
124A MET* 1.3 61.7 + - - +
126A GLY* 3.2 3.3 + - - -
127A ALA* 3.1 19.4 + - - +
184A LEU* 4.2 20.6 - - + -
186A THR* 5.6 0.2 - - - +
412A TYR* 3.7 35.6 - - + +
421A PHE* 3.6 10.5 - - + -
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Residues in contact with MET 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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32A LEU* 5.3 2.0 - - + -
109A VAL* 4.3 2.8 - - + +
120A THR 3.5 13.2 + - - +
121A ILE* 3.1 30.8 + - + +
123A PRO* 1.3 75.2 - - - +
125A VAL* 1.3 60.7 + - - +
127A ALA* 3.3 1.2 + - - +
128A ILE* 2.9 48.8 + - + +
134A VAL* 3.7 38.4 - - + +
136A LEU* 4.5 21.5 - - + -
153A ILE* 4.6 14.4 - - + -
157A LEU* 4.6 5.2 - - + -
162A TYR* 3.6 38.1 - - + +
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Residues in contact with VAL 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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29A LEU* 3.8 16.0 - - + +
32A LEU* 3.9 16.4 - - + -
66A VAL* 4.3 6.1 - - + +
69A GLU* 3.9 21.5 - - + -
70A ILE* 3.5 39.9 - - + -
73A MET* 3.9 11.0 - - + -
121A ILE* 2.8 23.2 + - + +
122A GLN* 3.5 10.5 - - - +
123A PRO 3.2 0.4 - - - -
124A MET* 1.3 76.8 - - - +
126A GLY* 1.3 56.4 + - - +
128A ILE* 3.5 4.0 + - - +
129A ALA* 3.0 27.2 + - - +
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Residues in contact with GLY 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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73A MET* 3.8 18.8 - - - +
122A GLN 3.5 5.5 + - - -
123A PRO 3.2 8.2 + - - -
125A VAL* 1.3 79.0 - - - +
127A ALA* 1.3 56.6 + - - +
129A ALA* 3.3 3.8 + - - +
130A ALA* 3.1 27.7 + - - +
417A SER* 3.9 20.4 - - - +
418A PHE* 4.6 1.9 - - - -
421A PHE* 3.7 7.2 - - - -
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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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107A VAL* 4.1 15.3 - - + -
109A VAL* 5.2 0.2 - - + -
123A PRO 3.1 14.8 + - - +
124A MET* 3.8 1.6 - - - +
126A GLY* 1.3 72.8 - - - +
128A ILE* 1.3 64.5 + - - +
130A ALA 3.3 2.8 + - - -
132A ASN* 3.0 29.3 + - - -
134A VAL* 3.5 25.8 - - + -
421A PHE* 3.5 30.1 - - + -
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Residues in contact with ILE 128 (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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25A ARG* 3.6 26.4 - - - +
28A GLN* 4.1 9.0 - - + -
29A LEU* 3.9 14.8 - - + -
32A LEU* 4.0 23.8 - - + -
124A MET* 2.9 37.7 + - + +
125A VAL* 3.7 3.8 - - - +
127A ALA* 1.3 76.4 - - - +
129A ALA* 1.3 58.0 + - - +
131A GLY* 2.9 21.7 + - - -
132A ASN 4.2 6.7 - - - -
134A VAL* 4.0 4.7 - - + -
157A LEU* 4.3 13.0 - - + -
162A TYR* 3.6 37.8 + - + +
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Residues in contact with ALA 129 (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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25A ARG* 2.9 26.2 + - - +
29A LEU* 4.5 10.5 - - + +
73A MET* 3.9 26.9 - - + -
77A LEU* 3.5 25.0 - - + +
80A TRP* 5.7 0.9 - - + -
125A VAL 3.0 18.3 + - - +
126A GLY 3.3 5.6 + - - +
128A ILE* 1.3 77.2 - - - +
130A ALA* 1.3 57.7 + - - +
131A GLY 3.2 0.2 - - - -
418A PHE* 3.6 9.5 - - + -
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Residues in contact with ALA 130 (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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25A ARG* 3.3 7.3 + - - -
102A GLU 4.6 0.2 - - - -
103A PRO* 3.3 25.5 - - - +
126A GLY 3.1 14.4 + - - +
128A ILE 3.2 0.6 - - - -
129A ALA* 1.3 76.0 - - - +
131A GLY* 1.3 58.3 + - - +
132A ASN* 3.3 8.3 - - - +
418A PHE* 3.8 16.9 - - + +
421A PHE* 3.3 22.9 - - + +
422A SER* 3.1 22.8 + - - +
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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