Contacts of the strand formed by residues 86 - 101 (chain C) 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 LYS 86 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82C ILE* 4.0 2.3 - - - +
83C SER 3.4 28.2 + - - +
85C PRO* 1.3 87.9 - - + +
87C VAL* 1.3 74.1 + - - +
88C LEU* 4.1 15.6 - - + +
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Residues in contact with VAL 87 (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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80C ASN* 5.6 7.9 - - + +
81C VAL 4.6 0.9 - - - +
82C ILE* 3.6 25.4 - - + -
85C PRO 5.1 2.5 - - - +
86C LYS* 1.3 85.6 - - - +
88C LEU* 1.3 67.8 + - - +
89C MET 4.9 6.5 - - - +
90C LYS* 6.3 5.2 - - + -
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Residues in contact with LEU 88 (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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81C VAL* 2.8 27.1 + - + +
83C SER* 3.5 34.5 - - - +
86C LYS* 4.1 23.8 - - + +
87C VAL* 1.3 82.2 - - - +
89C MET* 1.3 76.5 + - + +
169C PRO* 3.6 33.4 - - + -
172C PHE* 4.7 1.8 - - + -
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Residues in contact with MET 89 (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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80C ASN* 3.4 6.8 - - - +
81C VAL* 2.9 41.7 + - + +
87C VAL* 5.2 5.0 - - - +
88C LEU* 1.3 91.3 - - + +
90C LYS* 1.3 63.0 + - - +
92C ILE* 3.5 26.5 - - + -
166C VAL* 5.9 9.0 - - + +
169C PRO* 5.9 6.7 - - + -
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Residues in contact with LYS 90 (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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80C ASN* 4.1 11.7 - - - +
87C VAL* 6.3 6.1 - - + -
89C MET* 1.3 78.1 - - - +
91C GLN* 1.3 88.2 + - + +
92C ILE* 3.6 6.9 - - - +
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Residues in contact with GLN 91 (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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187A PRO 4.8 1.9 - - - +
188A ALA* 4.9 7.8 - - - +
78C MET* 3.4 30.7 - - + +
79C VAL 3.3 3.1 + - - -
80C ASN* 2.8 31.4 + - - +
90C LYS* 1.3 91.7 - - + +
92C ILE* 1.3 59.7 + - - +
93C PRO* 3.7 4.3 - - - +
177C THR* 2.8 30.1 + - - +
178C ALA* 5.9 1.4 - - - +
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Residues in contact with ILE 92 (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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77C ALA 3.1 4.2 - - - +
78C MET* 3.5 2.4 - - - -
79C VAL* 2.8 50.5 + - + +
81C VAL* 4.2 12.3 - - + +
89C MET* 3.5 53.4 - - + +
90C LYS 3.6 4.9 - - - +
91C GLN* 1.3 74.3 - - - +
93C PRO* 1.3 78.9 - - + +
94C ILE 3.6 0.3 + - - -
163C LEU* 4.3 11.2 - - + -
164C PRO* 4.1 22.2 - - + -
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Residues in contact with PRO 93 (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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70A SER* 5.9 2.9 - - - -
100A VAL* 6.0 0.3 - - - +
186A LEU* 3.9 32.0 - - + +
187A PRO* 3.1 27.6 - - + +
188A ALA* 5.0 5.4 - - + -
76C GLU* 4.6 10.1 - - + -
77C ALA 3.4 5.2 - - - +
78C MET* 3.4 20.6 - - + -
91C GLN 3.7 6.1 - - - +
92C ILE* 1.3 96.7 - - + +
94C ILE* 1.3 60.4 + - - +
95C TRP 4.0 1.0 + - - -
162C VAL 4.0 6.8 - - - +
163C LEU* 4.2 1.2 - - - +
164C PRO* 4.4 11.1 - - + +
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Residues in contact with ILE 94 (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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75C LEU 3.1 17.0 - - - +
76C GLU* 3.6 2.3 - - - -
77C ALA* 2.7 36.4 + - + +
79C VAL* 3.6 31.0 - - + -
92C ILE 3.9 5.6 - - - +
93C PRO* 1.3 75.6 - - - +
95C TRP* 1.3 58.5 + - - +
96C LEU* 3.2 30.0 + - + +
122C ILE* 4.6 9.9 - - + -
133C VAL* 4.9 4.3 - - + -
162C VAL* 3.7 22.7 - - + +
163C LEU* 3.6 14.8 - - + -
174C PHE* 3.6 21.3 - - + -
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Residues in contact with TRP 95 (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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72A ALA* 3.8 14.1 - - + +
74A ILE* 3.6 30.1 - - + +
95A TRP* 5.2 0.4 - + - -
97A PRO* 5.0 3.4 - - + +
99A GLY* 5.1 7.5 + - - -
100A VAL* 3.7 25.1 - - + -
184A GLN* 3.5 39.0 - - + -
186A LEU* 3.6 29.3 - - + +
74C ILE* 3.5 41.5 - - + -
75C LEU 4.0 1.1 - - - -
76C GLU* 5.0 4.3 - - + +
93C PRO 4.0 1.8 - - - -
94C ILE* 1.3 67.9 - - - +
96C LEU* 1.3 59.3 + - - +
97C PRO* 3.2 29.4 - - + +
161C PHE 5.5 1.1 - - - -
162C VAL* 3.2 30.5 + - - +
182C ILE* 4.0 17.3 - - + -
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Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ILE* 4.1 1.3 - - - +
75C LEU* 2.7 52.6 + - + +
77C ALA* 4.8 5.6 - - + -
94C ILE* 3.6 34.3 - - + +
95C TRP* 1.3 72.9 - - - +
97C PRO* 1.3 59.3 - - - +
98C LEU* 3.2 12.9 + - + +
122C ILE* 3.8 28.7 - - + -
133C VAL* 5.0 6.7 - - + +
135C VAL* 4.1 16.8 - - + +
157C PHE* 3.5 32.8 - - + -
162C VAL* 3.7 13.0 - - + -
179C LEU* 6.0 0.7 - - + -
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Residues in contact with PRO 97 (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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95A TRP* 4.8 5.8 - - + +
97A PRO* 4.3 28.7 - - + -
161A PHE* 3.8 7.8 - - + -
73C PHE 4.8 0.2 - - - +
74C ILE* 3.8 22.6 - - + -
95C TRP* 3.2 29.6 - - + +
96C LEU* 1.3 80.5 - - - +
98C LEU* 1.3 64.8 + - - +
99C GLY* 3.3 2.2 - - - +
155C GLN* 3.4 12.3 + - - -
157C PHE* 3.5 18.9 - - + -
161C PHE* 5.0 9.2 - - + -
162C VAL* 4.8 4.9 - - + -
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Residues in contact with LEU 98 (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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161A PHE* 3.5 6.4 - - - -
73C PHE* 2.7 34.7 + - + +
75C LEU* 3.7 35.7 - - + -
96C LEU* 3.2 17.9 + - + +
97C PRO* 1.3 73.0 - - - +
99C GLY* 1.3 57.1 + - - +
115C ILE* 4.3 19.7 - - + -
135C VAL* 5.1 4.3 - - + -
147C LEU* 3.9 20.1 - - + +
148C ARG 4.9 1.9 + - - -
149C LEU* 3.6 32.8 - - + -
150C LEU* 6.1 1.8 - - + -
155C GLN* 3.2 29.0 + - - +
157C PHE* 5.3 0.9 - - + -
181C LEU* 4.7 0.9 - - + -
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Residues in contact with GLY 99 (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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95A TRP* 5.1 8.9 - - - -
161A PHE* 4.3 16.8 - - - -
72C ALA* 3.4 5.3 - - - +
73C PHE* 2.9 31.1 + - - +
97C PRO* 3.3 4.5 - - - +
98C LEU* 1.3 80.3 - - - +
100C VAL* 1.3 64.7 + - - -
147C LEU* 3.5 8.0 - - - +
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Residues in contact with VAL 100 (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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93A PRO 5.9 0.9 - - - +
95A TRP* 3.5 32.1 - - + +
160A GLU 5.0 4.7 - - - +
161A PHE* 3.8 19.9 + - - +
162A VAL 4.0 16.6 - - - +
163A LEU 4.9 4.4 - - - +
164A PRO* 5.1 15.0 - - + -
165A PRO* 5.0 4.9 - - - +
70C SER* 4.9 6.3 - - - -
71C SER 3.7 5.4 - - - +
72C ALA* 5.2 0.4 - - + -
99C GLY* 1.3 76.2 - - - +
101C ALA* 1.3 66.8 + - - +
146C PRO* 3.8 13.3 - - - +
147C LEU* 3.5 11.8 - - - +
186C LEU* 3.8 25.6 - - + -
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Residues in contact with ALA 101 (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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70C SER* 3.6 3.1 - - - -
71C SER* 2.9 39.8 + - - +
73C PHE* 3.7 25.5 - - + -
100C VAL* 1.3 78.2 - - - +
102C ASP* 1.3 66.6 + - - +
103C GLN* 5.3 1.0 - - - +
111C THR* 4.7 4.3 - - + +
145C HIS* 4.5 8.5 - - + -
146C PRO* 4.2 11.7 - - + -
147C LEU* 4.2 12.3 - - + -
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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