Contacts of the strand formed by residues 167 - 175 (chain A) in PDB entry 1L4E
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 VAL 167 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A GLU* 3.4 23.6 - - + +
61A LYS 5.2 0.4 - - - -
62A ALA* 4.0 17.9 - - + -
111A HIS* 5.8 1.3 - - - +
162A LEU* 3.4 34.5 + - + +
163A ALA* 3.5 18.2 - - - +
165A ARG* 4.8 6.5 - - + +
166A GLY* 1.3 78.2 - - - +
168A THR* 1.3 63.6 + - - +
169A LEU 3.8 14.8 - - - +
170A PHE* 3.6 27.6 - - + -
258A LEU* 3.6 8.7 - - - +
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Residues in contact with THR 168 (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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51A GLY 5.2 2.7 - - - +
52A LEU* 3.8 22.0 - - + +
57A GLN* 4.1 8.4 + - + +
58A VAL* 3.5 8.7 - - - +
59A GLY* 2.7 32.2 + - - +
60A GLU 3.0 5.2 + - - -
166A GLY 3.7 11.0 - - - +
167A VAL* 1.3 78.8 - - - +
169A LEU* 1.3 60.3 + - - +
170A PHE* 4.4 0.9 - - - -
258A LEU* 3.6 17.8 - - + +
259A PRO* 3.3 27.5 - - - +
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Residues in contact with LEU 169 (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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58A VAL* 4.2 16.2 - - + -
60A GLU 3.5 1.4 + - - -
61A LYS* 3.5 27.4 - - + +
62A ALA 3.1 24.6 + - - +
167A VAL* 3.7 3.4 - - - +
168A THR* 1.3 81.5 + - - +
170A PHE* 1.3 76.1 + - - +
259A PRO* 3.9 25.4 - - + +
261A LEU* 4.0 25.8 - - + -
286A ILE* 4.9 1.3 - - + -
325A MET* 4.3 14.3 - - + +
328A VAL* 4.0 33.9 - - + -
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Residues in contact with PHE 170 (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 ALA* 3.3 6.5 - - + +
64A LEU* 4.0 19.1 - - + -
159A THR* 3.4 43.1 - - + -
160A CYS* 5.3 0.2 - - - -
162A LEU* 4.0 15.9 - - + -
163A ALA* 4.4 5.4 - - + -
167A VAL* 3.6 30.3 - - + -
169A LEU* 1.3 81.2 - - - +
171A GLY* 1.3 61.9 + - - +
249A VAL* 4.7 3.8 - - + -
253A ALA* 4.0 15.0 - - + -
256A CYS* 5.6 0.4 - - + -
258A LEU* 3.8 30.3 - - + -
259A PRO 3.1 15.9 + - - +
260A VAL* 3.5 16.9 - - + -
261A LEU* 2.8 28.6 + - - +
325A MET* 4.2 2.5 - - - -
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Residues in contact with GLY 171 (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 ALA 2.9 10.7 + - - +
63A VAL* 4.1 6.5 - - - -
64A LEU* 2.9 28.7 + - - +
170A PHE* 1.3 75.6 - - - +
172A VAL* 1.3 64.1 + - - +
249A VAL* 5.0 0.3 - - - +
261A LEU* 3.6 9.0 - - - -
321A ALA* 4.0 14.6 - - - -
325A MET* 4.1 8.3 - - - +
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Residues in contact with VAL 172 (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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63A VAL* 4.8 0.9 - - - -
64A LEU 3.7 3.8 - - - +
171A GLY* 1.3 73.2 - - - -
173A GLY* 1.3 59.0 + - - +
246A MET* 4.0 25.6 - - + +
249A VAL* 3.5 39.3 - - + -
250A MET* 3.9 22.2 - - + -
260A VAL* 3.8 14.6 - - + -
261A LEU 3.2 16.9 + - - +
262A LEU* 4.0 10.3 - - - -
263A ASP* 3.5 11.6 - - - +
267A SER* 4.1 3.6 - - - -
318A GLY* 3.5 14.8 - - - -
321A ALA* 4.2 2.1 - - - +
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Residues in contact with GLY 173 (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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63A VAL* 4.9 0.2 - - - +
64A LEU 2.9 12.7 + - - +
65A VAL* 3.9 4.3 - - - -
66A MET* 2.9 26.4 + - - +
172A VAL* 1.3 77.2 - - - +
174A GLU* 1.3 63.5 + - - +
246A MET* 3.6 12.3 - - - +
263A ASP* 4.9 1.3 - - - -
317A GLU 3.8 3.6 - - - -
318A GLY* 3.7 18.4 - - - -
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Residues in contact with GLU 174 (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 VAL* 4.0 3.5 - - - +
66A MET 3.2 12.6 - - - +
173A GLY* 1.3 75.8 - - - +
175A LEU* 1.3 63.7 + - - +
179A ASN* 2.8 26.3 + - - +
242A ASP* 4.5 8.1 - - + -
246A MET* 3.6 19.1 - - + -
263A ASP* 4.5 2.3 - - - +
266A LEU* 3.6 35.4 - - + +
316A GLY* 3.4 10.9 - - - -
317A GLU* 3.0 44.8 + - - +
990A RBZ 2.6 25.1 + - - -
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Residues in contact with LEU 175 (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 VAL* 4.3 2.9 - - + -
66A MET 2.9 5.9 + - - +
67A CYS* 3.1 23.4 - - - +
68A ALA 3.0 24.3 + - - -
85A THR* 3.8 14.6 - - + +
88A GLN* 3.5 22.2 - - + -
89A ALA* 3.5 36.1 - - - +
92A MET* 3.9 12.1 - - + -
174A GLU* 1.3 81.5 - - - +
176A GLY* 1.3 59.1 + - - +
177A MET* 4.8 2.2 - - + -
179A ASN* 4.2 2.2 - - - -
242A ASP* 4.4 0.9 - - - +
317A GLU* 4.2 7.4 - - + -
990A RBZ 3.8 37.9 - - + +
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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