Contacts of the strand formed by residues 70 - 82 (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 SER 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A GLY 5.6 0.3 + - - -
68A SER 3.7 5.5 + - - -
69A VAL* 1.3 77.8 - - - +
71A SER* 1.3 61.7 + - - +
100A VAL* 4.9 6.1 - - - -
101A ALA 3.6 13.5 - - - -
102A ASP* 3.5 23.3 - - - +
103A GLN* 4.8 0.6 + - - -
104A LYS* 5.9 0.3 - - - -
186A LEU* 2.8 41.5 + - - +
188A ALA* 4.8 5.9 - - - +
93C PRO* 5.9 2.0 - - - -
164C PRO* 4.5 17.2 - - - +
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Residues in contact with SER 71 (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* 3.2 35.0 + - - +
69A VAL* 4.2 6.8 + - - +
70A SER* 1.3 77.4 + - - +
72A ALA* 1.3 60.7 + - - +
73A PHE* 3.8 9.4 - - - -
100A VAL* 3.7 2.3 - - - +
101A ALA* 2.9 36.0 + - - +
103A GLN* 5.0 0.9 + - - +
108A PHE* 3.5 26.3 - - - -
183A THR* 4.1 1.3 - - - -
184A GLN 3.5 4.9 - - - -
186A LEU* 4.5 4.5 - - - -
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Residues in contact with ALA 72 (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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71A SER* 1.3 73.9 - - - +
73A PHE* 1.3 61.0 + - - +
74A ILE* 4.3 3.8 - - + -
99A GLY 3.4 8.7 - - - +
100A VAL* 4.5 0.7 - - - +
183A THR* 3.1 23.0 + - - -
184A GLN* 2.8 27.2 + - + +
186A LEU* 4.5 5.4 - - + +
95C TRP* 3.8 45.5 - - + -
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Residues in contact with PHE 73 (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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71A SER* 3.8 16.4 - - - -
72A ALA* 1.3 78.0 - - - +
74A ILE* 1.3 60.4 + - - +
98A LEU* 2.7 39.6 + - + -
99A GLY 2.9 20.9 + - - +
101A ALA* 3.7 23.8 - - + -
108A PHE* 3.4 43.5 - + - -
111A THR* 3.9 17.9 - - + -
112A THR* 4.5 6.1 - - + -
115A ILE* 3.8 17.3 - - + -
147A LEU* 3.7 29.2 - - + -
181A LEU* 4.4 12.8 - - + -
182A ILE 3.7 1.6 - - - -
183A THR* 3.9 11.2 - - - -
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Residues in contact with ILE 74 (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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72A ALA* 4.3 4.9 - - + +
73A PHE* 1.3 88.6 - - - +
75A LEU* 1.3 71.8 + - - +
76A GLU 4.8 0.2 - - - +
95A TRP* 3.5 51.1 - - + -
96A LEU 3.5 11.9 - - - +
97A PRO* 3.8 15.7 - - + -
98A LEU 4.0 0.4 - - - +
181A LEU* 3.5 5.5 - - - +
182A ILE* 2.8 49.9 + - + +
184A GLN* 5.3 2.9 - - + -
95C TRP* 3.6 34.5 - - + +
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Residues in contact with LEU 75 (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* 4.7 2.7 - - + -
74A ILE* 1.3 74.8 - - - +
76A GLU* 1.3 59.8 + - - +
77A ALA 3.8 0.8 + - - -
94A ILE 3.1 3.8 - - - +
95A TRP* 4.0 0.3 - - - -
96A LEU* 2.7 52.9 + - + +
98A LEU* 3.7 33.4 - - + +
115A ILE* 4.7 6.5 - - + -
120A TYR* 5.0 9.9 - - + -
135A VAL* 5.0 9.4 - - + -
149A LEU* 4.1 12.3 - - + -
179A LEU* 4.0 30.7 - - + -
180A LYS 3.5 15.7 - - - +
181A LEU* 3.7 26.2 - - + -
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Residues in contact with GLU 76 (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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74A ILE* 4.2 1.4 + - - +
75A LEU* 1.3 69.5 - - - +
77A ALA* 1.3 60.7 + - - +
78A MET* 3.8 11.0 + - + +
93A PRO* 4.6 13.2 - - + -
94A ILE 3.6 6.5 - - - +
95A TRP* 5.0 5.4 - - + +
178A ALA 4.0 0.3 - - - +
179A LEU* 3.7 2.5 - - - -
180A LYS* 2.9 60.7 + - + +
182A ILE* 3.4 31.3 - - + +
184C GLN* 5.0 1.9 + - - -
185C PRO 4.7 1.9 - - - +
186C LEU* 3.8 22.6 - - + +
187C PRO* 3.3 31.9 - - - +
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Residues in contact with ALA 77 (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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75A LEU 3.8 0.2 + - - -
76A GLU* 1.3 72.0 - - - +
78A MET* 1.3 62.0 + - - +
79A VAL* 3.7 7.0 - - + -
92A ILE 3.1 5.0 - - - +
93A PRO* 4.3 1.8 - - - -
94A ILE* 2.7 49.1 + - + +
96A LEU* 4.8 10.8 - - + -
122A ILE* 5.0 6.1 - - + -
176A LEU* 3.9 20.9 - - + -
178A ALA 3.5 4.3 - - - -
179A LEU* 3.9 13.0 - - + -
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Residues in contact with MET 78 (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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76A GLU* 3.8 11.6 + - + +
77A ALA* 1.3 68.8 - - - +
79A VAL* 1.3 57.9 + - - +
91A GLN* 3.4 47.1 - - - +
92A ILE 3.5 4.5 - - - -
93A PRO* 3.4 36.8 - - + -
177A THR* 2.4 37.7 + - - +
178A ALA* 2.9 25.0 + - + +
187C PRO* 3.6 33.4 - - + +
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Residues in contact with VAL 79 (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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77A ALA* 3.8 6.7 - - + +
78A MET* 1.3 77.4 - - - +
80A ASN* 1.3 72.6 + - - +
81A VAL* 4.6 3.6 - - + -
91A GLN 3.3 0.7 + - - -
92A ILE* 2.8 44.9 + - + +
94A ILE* 3.6 28.3 - - + -
122A ILE* 4.9 4.5 - - + -
163A LEU* 5.8 0.4 - - + -
174A PHE* 3.5 33.0 - - + -
175A ASP 3.4 10.1 - - - +
176A LEU* 3.7 24.9 - - + +
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Residues in contact with ASN 80 (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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79A VAL* 1.3 73.4 - - - +
81A VAL* 1.3 63.7 + - - +
82A ILE* 3.5 8.3 + - + +
89A MET 3.4 8.5 - - - +
90A LYS* 4.3 11.7 - - - +
91A GLN* 2.8 40.7 + - - +
174A PHE* 4.9 0.2 - - - -
175A ASP* 2.9 51.5 + - + +
177A THR* 3.6 17.7 - - - +
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Residues in contact with VAL 81 (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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79A VAL* 4.6 1.8 - - + -
80A ASN* 1.3 71.4 - - - +
82A ILE* 1.3 55.6 + - - +
88A LEU* 2.8 43.5 + - + -
89A MET* 2.9 30.0 + - + +
92A ILE* 4.2 14.3 - - + +
163A LEU* 6.3 2.0 - - + -
169A PRO* 5.8 1.8 - - + -
172A PHE* 3.5 42.6 - - + -
173A THR 3.7 3.4 - - - -
174A PHE* 4.2 24.7 - - + +
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Residues in contact with ILE 82 (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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80A ASN* 4.0 14.4 - - + +
81A VAL* 1.3 79.0 - - - +
83A SER* 1.3 61.0 + - - +
84A GLY 4.6 14.6 - - - +
85A PRO 5.7 4.9 - - - +
88A LEU* 4.2 8.1 - - - +
172A PHE* 3.5 4.3 - - - +
173A THR* 2.9 62.1 + - + +
174A PHE 4.8 2.7 - - - +
175A ASP* 4.4 20.0 - - + +
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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