Contacts of the strand formed by residues 137 - 145 (chain C) in PDB entry 4LL1
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 GLN 137 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C PHE* 3.9 27.3 - - + +
127C ALA 3.9 0.3 - - - +
128C PHE* 3.3 6.8 - - - +
129C LEU* 2.9 52.0 + - + +
131C ARG* 4.8 12.1 + - - +
135C PRO 3.6 3.8 + - - +
136C THR* 1.3 74.1 - - - +
138C GLU* 1.3 72.5 + - - +
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Residues in contact with GLU 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C PHE* 4.0 4.0 - - - -
126C LYS* 3.8 27.0 + - + +
127C ALA 3.4 3.6 - - - +
128C PHE* 3.7 34.2 - - + -
136C THR* 4.0 5.1 + - - +
137C GLN* 1.3 85.1 + - - +
139C THR* 1.3 63.3 + - - +
140C LYS* 5.8 0.3 - - - +
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Residues in contact with THR 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C PHE* 3.5 48.7 + - + +
11C GLU* 4.3 4.7 - - - +
12C VAL* 4.2 14.5 + - + +
125C VAL 4.0 0.3 - - - +
126C LYS* 3.2 6.1 - - - +
127C ALA* 2.8 49.6 + - + +
138C GLU* 1.3 75.6 - - - +
140C LYS* 1.3 64.3 + - - +
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Residues in contact with LYS 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C VAL* 5.3 0.9 - - - -
124C TRP* 3.8 37.7 - - + +
125C VAL 3.4 7.4 - - - +
126C LYS* 3.6 36.4 - - + +
138C GLU* 5.8 0.2 - - - +
139C THR* 1.3 80.4 + - - +
141C LYS* 1.3 66.6 + - - +
142C ASN* 3.8 13.9 - - - +
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Residues in contact with LYS 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C GLU* 2.6 33.6 + - - -
12C VAL* 2.9 35.4 + - + +
13C VAL* 4.7 4.2 - - - +
14C PHE* 3.8 26.9 - - + +
124C TRP* 4.0 2.9 - - - -
125C VAL 2.8 39.1 + - - -
140C LYS* 1.3 74.6 - - - +
142C ASN* 1.3 70.2 + - - +
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Residues in contact with ASN 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C PHE* 3.5 9.9 - - - -
122C ASP* 5.2 5.5 - - - +
123C TYR 3.2 10.1 + - - +
124C TRP* 3.5 22.4 - - - +
140C LYS* 3.8 16.4 - - - +
141C LYS* 1.3 83.2 - - - +
143C PHE* 1.3 64.6 + - - +
144C GLU* 4.7 9.0 - - - +
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Residues in contact with PHE 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C PHE* 3.7 32.5 - + + -
19C LYS 5.7 0.2 - - - +
21C TYR* 3.8 26.9 - + + -
27C VAL* 4.2 7.4 - - + -
70C LEU* 3.9 14.6 - - + -
103C PHE* 4.0 13.9 - + - -
105C LEU* 4.1 9.2 - - + -
113C SER* 4.0 3.6 + - - -
123C TYR* 3.0 50.0 + + + +
124C TRP* 3.6 31.0 - - - -
125C VAL* 4.0 8.1 - - + -
142C ASN* 1.3 75.3 - - - +
144C GLU* 1.3 69.6 + - - +
145C VAL* 3.7 15.7 - - + -
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Residues in contact with GLU 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LYS 4.5 6.8 + - - +
20C VAL* 3.4 26.1 - - + -
21C TYR* 2.8 38.0 + - - -
113C SER* 3.2 25.4 - - - +
142C ASN* 4.7 10.4 - - - +
143C PHE* 1.3 83.0 - - - +
145C VAL* 1.3 56.7 + - - +
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Residues in contact with VAL 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C VAL* 4.0 5.4 - - - +
21C TYR* 3.2 9.6 - - + +
105C LEU* 4.2 8.3 - - + -
110C LEU* 3.1 34.5 - - + -
111C GLY 3.9 14.8 - - - +
112C THR* 3.5 3.6 - - - +
113C SER* 3.0 29.0 + - - +
123C TYR* 3.6 41.7 - - + -
143C PHE* 3.7 15.0 - - + -
144C GLU* 1.3 80.2 - - - +
146C VAL* 1.3 67.1 + - - +
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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