Contacts of the helix formed by residues 129 - 140 (chain A) in PDB entry 4LQL
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 129 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A MET* 3.4 22.4 - - - +
82A THR 3.9 5.2 - - - -
83A PHE* 3.9 31.3 - - - -
84A SER 4.5 2.9 + - - +
125A GLN 3.6 2.4 + - - -
126A SER* 3.2 3.3 + - - -
128A HIS* 1.3 78.9 - - - +
130A ASP* 1.3 62.6 + - - +
131A ARG 3.3 0.4 - - - -
132A GLU* 4.0 4.9 - - - +
133A TYR 3.5 12.6 + - - -
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Residues in contact with ASP 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TRP* 5.1 2.0 - - + -
80A MET* 4.3 19.7 - - + +
102A HIS* 5.0 11.1 - - + -
103A LEU 5.3 0.4 - - - +
104A ALA* 4.4 27.4 - - + -
126A SER* 3.1 16.2 + - - +
129A GLY* 1.3 75.2 - - - +
131A ARG* 1.3 55.0 + - - +
132A GLU 3.4 0.2 - - - -
133A TYR* 3.2 12.0 - - + +
134A ALA* 2.6 30.8 + - - +
440C MET* 4.7 4.5 - - - +
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Residues in contact with ARG 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A SER 4.5 1.2 + - - -
127A ALA 3.4 16.5 + - - -
128A HIS* 4.2 12.3 - - - +
129A GLY 3.3 1.0 - - - +
130A ASP* 1.3 76.0 - - - +
132A GLU* 1.3 60.4 + - - +
134A ALA* 3.0 23.8 + - - +
135A TYR* 3.2 6.9 + - - +
332C ASP* 2.3 35.1 + - - +
344C ILE* 4.9 3.2 - - - +
426C TRP* 5.7 3.2 - - - -
432C LEU* 6.1 2.6 - - - +
435C GLY 4.7 1.0 + - - -
436C ALA* 3.7 35.5 - - - +
439C TRP* 3.8 31.4 - - + +
440C MET* 4.7 12.6 - - + +
444C GLY 3.7 21.8 - - - +
445C GLY* 4.3 18.5 + - - +
446C HIS* 4.7 2.6 - - + +
448C THR* 6.3 1.0 - - - +
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Residues in contact with GLU 132 (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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83A PHE* 3.6 15.4 - - + -
84A SER 4.3 0.6 - - - +
85A PRO* 3.0 11.3 - - - +
86A ALA* 2.5 44.7 + - - +
128A HIS 3.9 5.9 + - - +
129A GLY 4.0 3.1 - - - +
131A ARG* 1.3 74.5 - - - +
133A TYR* 1.3 67.6 + - - +
134A ALA 3.0 1.1 + - - -
135A TYR* 3.2 15.0 + - + +
136A ILE 3.8 2.4 + - - -
188C VAL* 3.8 10.3 - - + -
189C ALA* 2.8 32.1 + - - +
190C VAL* 3.0 17.7 + - - +
445C GLY* 5.7 2.2 - - - -
446C HIS* 3.7 29.0 + - + +
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Residues in contact with TYR 133 (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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78A THR* 4.8 11.2 - - - -
80A MET* 3.9 17.9 - - + -
84A SER 5.8 1.3 + - - -
86A ALA* 4.5 4.2 - - - +
89A TRP* 5.8 11.4 - + - +
100A LEU* 6.4 1.3 - - + -
102A HIS* 4.4 20.0 - + + -
129A GLY 3.5 9.4 + - - +
130A ASP* 3.2 21.0 + - + +
132A GLU* 1.3 75.7 - - - +
134A ALA* 1.3 64.4 + - - +
136A ILE* 3.0 28.9 + - + +
137A ASN* 3.5 10.2 + - + +
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Residues in contact with ALA 134 (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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102A HIS* 6.1 2.5 - - + -
130A ASP 2.6 17.3 + - - +
131A ARG* 3.0 15.3 - - - +
132A GLU 3.0 1.6 - - - -
133A TYR* 1.3 75.7 - - - +
135A TYR* 1.3 60.6 + - - +
136A ILE 3.0 0.9 + - - -
137A ASN* 3.5 10.2 + - - +
138A SER* 3.6 14.9 + - - -
440C MET* 3.5 47.8 - - + +
443C GLY 4.8 2.2 - - - +
444C GLY 4.9 1.1 - - - +
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Residues in contact with TYR 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ALA* 6.1 0.4 - - + -
131A ARG 3.2 10.2 + - - +
132A GLU* 3.2 12.0 + - + +
134A ALA* 1.3 74.0 - - - +
136A ILE* 1.3 64.5 - - + +
138A SER* 3.9 0.7 - - - -
139A ARG* 2.9 36.4 + - + +
189C ALA* 5.3 4.9 - - + -
190C VAL* 4.6 24.5 - - - +
394C SER* 5.6 8.1 - - - -
396C PHE* 6.3 2.0 - + - -
443C GLY* 4.6 23.7 + - - -
444C GLY 5.4 3.4 - - - +
445C GLY* 5.9 2.0 - - - -
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Residues in contact with ILE 136 (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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86A ALA* 3.5 33.2 - - + +
89A TRP* 4.6 11.0 - - + -
90A ILE* 3.5 45.3 - - + +
93A THR* 5.8 2.9 - - - +
132A GLU 4.2 0.2 - - - +
133A TYR* 3.0 22.2 - - + +
135A TYR* 1.3 81.2 - - + +
137A ASN* 1.3 61.4 + - + +
138A SER 3.1 7.8 + - - -
139A ARG* 4.6 12.1 - - + -
140A LEU* 3.4 24.1 + - + +
189C ALA* 4.9 13.2 - - + -
196F VAL* 6.4 0.7 - - - -
200F ILE* 5.4 1.3 - - + -
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Residues in contact with ASN 137 (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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93A THR* 6.3 3.1 - - - -
100A LEU* 4.2 25.4 - - + -
102A HIS* 6.5 0.9 - - + -
133A TYR* 3.5 11.4 + - + +
134A ALA* 3.5 6.4 + - - +
136A ILE* 1.3 80.1 - - + +
138A SER* 1.3 58.2 + - - +
140A LEU* 4.9 0.7 - - - -
142A VAL* 3.4 36.6 + - + +
144A ALA* 4.2 9.1 - - + +
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Residues in contact with SER 138 (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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134A ALA 3.6 15.0 - - - -
135A TYR 3.9 2.0 - - - -
136A ILE 3.1 1.0 + - - -
137A ASN* 1.3 81.4 - - - +
139A ARG* 1.3 62.5 + - - +
140A LEU 3.0 1.1 - - - +
141A ASN* 2.7 32.7 + - - +
440C MET 4.8 0.2 - - - -
441C LYS* 3.8 25.4 - - - -
443C GLY 4.2 13.9 - - - -
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Residues in contact with ARG 139 (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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135A TYR* 2.9 28.5 + - + +
136A ILE* 4.5 9.9 - - + +
138A SER* 1.3 77.5 - - - +
140A LEU* 1.3 60.1 + - - +
141A ASN* 3.2 5.4 + - - -
395C TYR 3.2 18.4 + - - +
396C PHE* 4.3 13.9 - - + +
397C ASP* 3.5 44.2 - - - +
194F ASP* 2.8 29.9 + - - +
196F VAL* 4.3 8.0 - - - +
197F ALA* 3.3 30.9 - - - +
200F ILE* 4.0 20.3 - - + +
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Residues in contact with LEU 140 (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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90A ILE* 5.8 2.9 - - + -
93A THR* 4.4 17.7 - - - +
94A GLU* 4.9 8.3 - - + -
136A ILE* 3.4 19.3 + - + +
137A ASN* 4.9 1.6 - - - -
138A SER 3.0 0.6 - - - -
139A ARG* 1.3 79.2 - - + +
141A ASN* 1.3 70.8 + - - +
142A VAL* 4.6 7.0 - - + +
200F ILE* 4.4 26.5 - - + -
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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