Contacts of the strand formed by residues 173 - 186 (chain A) in PDB entry 4LDD
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 THR 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A THR* 3.7 29.9 + - - +
47A PRO 4.4 6.9 + - - -
48A SER* 4.7 0.2 - - - -
81A VAL* 3.7 3.5 - - - -
82A ILE* 2.9 60.3 + - + +
83A SER* 5.5 0.2 - - - -
84A GLY 5.5 4.0 - - - +
122A ILE 5.5 0.2 + - - -
124A HIS* 5.2 1.3 - - - -
172A PHE* 1.3 78.6 - - - +
174A PHE* 1.3 78.3 + - - +
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Residues in contact with PHE 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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48A SER* 3.4 33.2 - - - -
49A ASN* 4.0 1.7 + - - +
79A VAL* 3.5 26.9 - - + -
80A ASN 3.9 1.1 - - - -
81A VAL* 4.2 15.9 - - + -
82A ILE* 4.8 3.4 - - - +
94A ILE* 3.6 20.0 - - + -
122A ILE* 3.5 33.2 - - + -
124A HIS* 3.5 34.8 - - + -
133A VAL* 3.9 22.7 - - + -
163A LEU* 4.7 8.7 - - + -
172A PHE* 4.0 14.4 - + - -
173A THR* 1.3 88.2 + - - +
175A ASP* 1.3 61.2 + - - +
176A LEU 5.0 0.4 - - - +
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Residues in contact with ASP 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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49A ASN* 3.5 19.9 + - - +
79A VAL* 3.4 2.1 - - - -
80A ASN* 2.9 57.3 + - + +
82A ILE* 4.4 18.1 - - + +
174A PHE* 1.3 72.9 - - - +
176A LEU* 1.3 61.4 + - - +
177A THR* 3.2 11.2 + - - +
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Residues in contact with LEU 176 (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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48A SER* 4.5 6.0 - - - +
49A ASN* 2.8 41.1 + - - +
51A LEU* 3.6 38.8 - - + +
77A ALA* 3.9 11.0 - - + -
78A MET 4.2 0.9 - - - -
79A VAL* 3.7 25.3 - - + +
120A TYR* 3.9 19.1 - - + +
122A ILE* 4.7 15.3 - - + -
174A PHE* 4.0 1.2 - - + -
175A ASP* 1.3 69.4 - - - +
177A THR* 1.3 59.9 + - - +
178A ALA 3.6 23.6 - - - +
179A LEU* 4.8 11.9 - - + -
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Residues in contact with THR 177 (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 LEU* 3.8 7.8 - - - +
78A MET* 2.4 32.9 + - - +
80A ASN* 3.6 20.0 - - - +
91A GLN* 2.8 31.6 + - - +
175A ASP* 3.5 21.1 - - - +
176A LEU* 1.3 76.0 - - - +
178A ALA* 1.3 63.6 + - - +
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Residues in contact with ALA 178 (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 LEU* 3.8 8.0 - - - +
54A ILE* 5.2 10.5 - - + -
76A GLU 4.6 0.4 - - - -
77A ALA* 3.5 3.3 - - - -
78A MET* 2.9 38.6 + - + -
91A GLN* 5.9 1.3 - - - +
176A LEU* 3.6 6.1 - - - +
177A THR* 1.3 85.1 + - - +
179A LEU* 1.3 62.0 + - - +
180A LYS 4.3 0.7 - - - -
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Residues in contact with LEU 179 (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 LEU* 4.1 18.9 - - + +
52A ARG 4.3 5.5 + - - +
53A PRO* 3.3 21.6 - - + +
54A ILE* 2.7 42.6 + - - +
75A LEU* 4.0 31.6 - - + -
76A GLU 3.7 2.9 - - - +
77A ALA* 3.9 23.3 - - + -
96A LEU* 6.0 1.1 - - + -
120A TYR* 3.8 37.9 - - + -
176A LEU* 4.8 9.2 - - + -
178A ALA* 1.3 76.1 - - - +
180A LYS* 1.3 55.7 + - - +
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Residues in contact with LYS 180 (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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53A PRO* 5.2 0.2 - - - -
54A ILE* 3.3 12.1 - - + +
56A ASP* 3.5 42.7 + - + +
57A ASP* 5.3 1.9 + - - -
75A LEU* 3.4 10.4 - - - +
76A GLU* 2.9 65.6 + - + +
179A LEU* 1.3 74.3 - - - +
181A LEU* 1.3 62.4 + - - +
182A ILE* 3.8 14.7 + - + +
184C GLN* 5.8 2.6 - - - +
187C PRO* 5.5 4.6 - - - +
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Residues in contact with LEU 181 (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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53A PRO* 4.8 1.3 - - + -
54A ILE 2.9 11.2 + - - +
55A ALA* 4.7 3.4 - - + -
56A ASP* 3.2 25.8 + - - +
59A ILE* 3.3 11.3 - - + +
73A PHE* 4.4 17.3 - - + -
74A ILE 3.5 21.3 - - - +
75A LEU* 3.7 17.3 - - + -
98A LEU* 4.8 0.2 - - + -
112A THR* 4.7 11.4 - - + -
115A ILE* 3.9 28.0 - - + -
116A MET* 3.6 36.8 - - + -
179A LEU 4.3 0.4 + - - -
180A LYS* 1.3 71.7 - - - +
182A ILE* 1.3 68.7 + - - +
183A THR* 5.4 2.5 - - + -
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Residues in contact with ILE 182 (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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56A ASP* 4.3 14.6 - - - +
58A THR* 5.3 2.5 - - - +
59A ILE* 5.9 0.4 - - + -
73A PHE* 3.7 1.2 - - - -
74A ILE* 2.8 50.6 + - + +
76A GLU* 3.4 31.2 - - + +
95A TRP* 4.0 25.1 - - + -
180A LYS* 3.8 20.6 - - + +
181A LEU* 1.3 80.9 - - - +
183A THR* 1.3 71.5 + - - +
184A GLN* 6.1 0.9 - - + -
184C GLN* 4.4 19.5 - - - +
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Residues in contact with THR 183 (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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59A ILE* 3.7 38.3 - - + +
64A HIS* 3.0 33.7 + - + +
71A SER* 4.1 1.6 - - - -
72A ALA 3.1 12.1 + - - -
73A PHE* 3.9 13.3 - - - -
74A ILE* 5.4 0.9 - - - -
108A PHE* 3.7 15.7 - - + -
181A LEU* 5.4 2.7 - - + -
182A ILE* 1.3 83.4 - - - +
184A GLN* 1.3 68.1 + - - +
185A PRO* 4.3 1.6 - - - +
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Residues in contact with GLN 184 (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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64A HIS* 3.8 3.8 - - - -
71A SER* 3.5 0.2 - - - -
72A ALA* 2.8 38.2 + - + +
74A ILE* 5.3 2.4 - - + +
182A ILE* 6.1 0.9 - - + -
183A THR* 1.3 81.4 + - - +
185A PRO* 1.3 87.2 + - - +
186A LEU* 3.8 1.9 + - + +
56C ASP* 5.2 5.1 + - - -
58C THR* 5.9 1.2 + - - +
76C GLU* 4.8 2.2 + - - -
95C TRP* 3.5 38.6 - - + -
180C LYS* 5.9 2.2 - - - +
182C ILE* 4.2 23.1 - - + +
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Residues in contact with PRO 185 (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 SER* 4.1 28.7 - - - +
64A HIS* 3.4 28.9 - - + +
69A VAL* 4.3 7.0 - - + -
70A SER 4.0 4.0 - - - +
183A THR 4.3 1.3 - - - +
184A GLN* 1.3 110.4 + - - +
186A LEU* 1.3 68.8 + - - +
187A PRO* 4.1 4.6 - - - +
76C GLU* 4.7 1.2 - - - +
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Residues in contact with LEU 186 (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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69A VAL* 3.7 9.2 - - - +
70A SER* 2.8 40.6 + - - +
71A SER 4.5 5.6 - - - -
72A ALA* 4.5 1.8 - - + +
100A VAL* 3.8 29.6 - - + -
184A GLN 4.0 6.5 - - - +
185A PRO* 1.3 83.9 - - - +
187A PRO* 1.3 71.0 - - + +
188A ALA* 3.6 1.4 + - - +
76C GLU* 4.1 19.5 - - + +
93C PRO* 3.9 25.4 - - + +
95C TRP* 3.6 43.3 - - + -
164C PRO* 6.5 0.2 - - + -
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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