Contacts of the strand formed by residues 60 - 68 (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 GLU 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A GLY* 1.3 78.8 - - - +
61A LYS* 1.3 63.2 + - - +
107A GLY 5.5 3.0 - - - +
165A ARG 4.5 7.9 - - - +
166A GLY* 3.1 25.0 + - - +
167A VAL* 3.4 15.9 - - + +
168A THR* 3.0 23.0 + - - -
169A LEU 3.5 5.5 + - - -
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Residues in contact with LYS 61 (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* 3.6 17.7 - - + -
59A GLY 3.8 14.6 - - - -
60A GLU* 1.3 80.9 + - - +
62A ALA* 1.3 62.1 + - - +
106A ALA 2.7 27.0 + - - +
107A GLY* 3.6 19.6 + - - +
108A ALA* 3.4 15.8 - - + -
109A LYS* 3.0 23.6 + - - +
167A VAL* 4.5 1.1 - - - +
169A LEU* 3.5 21.3 - - + +
325A MET* 3.9 17.5 - - + -
329A GLU* 2.8 32.6 + - - +
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Residues in contact with ALA 62 (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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61A LYS* 1.3 77.1 - - - +
63A VAL* 1.3 63.2 + - - +
64A LEU* 4.1 11.3 + - + +
109A LYS* 3.3 10.5 - - + +
111A HIS* 4.1 21.1 - - + +
162A LEU* 4.6 2.0 - - + -
167A VAL* 4.0 22.6 - - + +
169A LEU 3.1 7.7 + - - +
170A PHE* 3.3 8.4 - - + +
171A GLY* 2.9 23.6 + - - +
325A MET* 3.9 1.8 - - - +
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Residues in contact with VAL 63 (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* 1.3 77.2 - - - +
64A LEU* 1.3 61.2 + - - +
65A VAL* 3.8 18.3 + - + -
99A VAL* 5.1 3.4 - - + +
103A ALA* 4.7 4.5 - - + -
108A ALA* 4.6 7.0 - - + -
109A LYS 2.9 9.8 + - - +
110A VAL* 3.5 12.3 - - + +
111A HIS 2.8 32.6 + - - +
171A GLY* 3.3 15.5 - - - +
172A VAL 4.8 0.4 - - - -
317A GLU 4.4 8.5 - - - +
318A GLY* 4.4 13.2 - - - +
322A ALA* 4.5 19.5 - - + +
325A MET* 3.9 23.3 - - + -
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Residues in contact with LEU 64 (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* 4.1 14.6 - - + +
63A VAL* 1.3 75.8 - - - +
65A VAL* 1.3 59.8 + - - +
66A MET* 3.8 9.6 + - - +
111A HIS* 3.5 17.7 - - + +
113A ILE* 4.4 7.6 - - + -
155A VAL* 5.3 0.7 - - + -
158A TYR* 4.3 18.4 - - + -
159A THR* 3.6 26.2 - - + +
162A LEU* 4.2 10.5 - - + -
170A PHE* 4.0 21.5 - - + -
171A GLY 2.9 13.8 + - - +
172A VAL* 3.7 2.3 - - - -
173A GLY 2.9 26.6 + - - +
249A VAL* 3.7 27.3 - - + +
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Residues in contact with VAL 65 (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* 4.1 8.7 - - + -
64A LEU* 1.3 73.2 - - - +
66A MET* 1.3 62.6 + - - +
67A CYS* 3.7 14.8 + - - -
92A MET* 4.2 18.8 - - + -
99A VAL* 4.5 5.4 - - + -
110A VAL* 3.9 25.8 - - + -
111A HIS 2.9 10.3 + - - +
112A VAL* 3.8 4.7 - - + -
113A ILE* 2.8 30.7 + - - +
173A GLY 3.5 2.9 - - - -
174A GLU 4.0 26.7 - - - +
317A GLU 3.5 20.6 - - - +
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Residues in contact with MET 66 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A LEU* 4.4 6.5 - - - +
65A VAL* 1.3 75.3 - - - +
67A CYS* 1.3 60.8 + - - +
113A ILE* 3.6 30.7 - - + -
115A VAL* 3.4 31.0 - - + -
155A VAL* 4.2 10.1 - - + -
172A VAL* 6.4 0.2 - - + -
173A GLY 2.9 14.5 + - - +
174A GLU* 3.2 5.7 - - - +
175A LEU 2.9 21.7 + - - +
242A ASP* 3.7 24.8 - - + +
245A GLY* 3.7 14.4 - - - -
246A MET* 3.7 23.8 - - + +
249A VAL* 4.3 18.2 - - + -
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Residues in contact with CYS 67 (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* 3.8 9.6 - - - -
66A MET* 1.3 76.5 - - - +
68A ALA* 1.3 63.1 + - - +
85A THR* 4.6 2.5 - - + -
89A ALA* 4.3 4.0 - - - -
112A VAL* 3.8 29.2 - - - -
113A ILE 2.8 14.3 + - - +
115A VAL* 3.0 25.9 + - - +
116A GLY 3.4 1.7 + - - -
117A ILE* 3.6 26.2 - - + +
125A VAL* 5.8 0.2 - - - -
175A LEU* 3.1 34.8 - - + +
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Residues in contact with ALA 68 (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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66A MET 4.3 0.4 + - - -
67A CYS* 1.3 77.2 - - - +
69A ASP* 1.3 67.8 + - - +
70A HIS* 3.5 7.0 + - - +
85A THR* 4.0 2.8 - - - +
115A VAL* 3.8 15.3 - - + -
116A GLY 3.5 17.9 - - - +
117A ILE* 3.9 3.2 - - - +
175A LEU 3.0 5.9 + - - -
176A GLY* 3.1 24.9 - - - -
241A PHE* 3.8 16.8 - - + +
242A ASP* 3.8 13.1 - - + +
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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