Contacts of the helix formed by residues 89 - 102 (chain A) in PDB entry 6LGV
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 PRO 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A ARG 3.5 5.3 - - - +
88A MET* 1.3 85.1 - - + +
90A PRO* 1.3 73.7 - - + +
91A ASP* 3.4 10.8 - - - +
92A LEU* 3.2 24.5 + - + -
93A SER* 2.8 29.1 + - - -
215A VAL* 5.2 8.5 - - + -
274A LEU* 4.3 8.7 - - + -
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Residues in contact with PRO 90 (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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88A MET 4.6 0.2 - - - +
89A PRO* 1.3 89.1 - - + +
91A ASP* 1.4 58.3 + - - +
93A SER* 3.4 7.1 + - - -
94A ALA* 2.9 28.1 + - - +
146A ASP* 3.9 20.1 + - + +
148A THR* 3.5 27.6 - - + +
149A ILE* 3.5 18.9 - - + +
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Residues in contact with ASP 91 (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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89A PRO* 4.2 8.7 - - - +
90A PRO* 1.4 73.0 - - - +
92A LEU* 1.3 79.2 + - - +
94A ALA* 3.3 3.0 + - - +
95A GLY 3.1 17.5 + - - -
149A ILE* 3.7 15.0 - - + +
271A PHE* 5.0 3.8 - - + -
272A SER* 2.7 35.3 + - - +
274A LEU* 3.4 24.7 - - - +
275A ALA* 3.4 15.5 - - + +
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Residues in contact with LEU 92 (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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88A MET* 3.9 24.7 - - + -
89A PRO* 3.2 22.8 + - + +
91A ASP* 1.3 84.4 + - - +
93A SER* 1.3 60.3 + - - +
95A GLY* 3.3 2.8 + - - +
96A MET* 3.1 18.7 + - - +
215A VAL* 3.8 25.8 - - + -
218A VAL* 5.3 1.3 - - + -
219A VAL* 3.7 28.3 - - + -
274A LEU* 3.7 39.0 - - + +
277A LEU* 4.5 1.8 - - + -
278A PRO* 3.7 20.2 - - + +
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Residues in contact with SER 93 (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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83A ALA* 3.5 24.7 + - - +
88A MET* 2.9 32.5 + - - +
89A PRO 2.8 10.9 + - - -
90A PRO* 3.5 8.1 - - - -
92A LEU* 1.3 76.2 - - - +
94A ALA* 1.3 60.9 + - - +
96A MET* 3.1 4.4 + - - +
97A VAL* 2.9 34.3 + - - +
145A VAL* 6.2 1.1 - - - -
146A ASP* 5.9 5.4 - - - -
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Residues in contact with ALA 94 (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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90A PRO 2.9 20.1 + - - +
91A ASP 3.3 6.0 + - - +
93A SER* 1.3 71.6 - - - +
95A GLY* 1.3 58.0 + - - +
97A VAL* 3.4 5.1 + - - +
98A LEU* 2.9 30.3 + - - +
141A THR* 4.8 0.9 - - - +
145A VAL* 3.9 29.1 - - + +
146A ASP 6.1 0.2 - - - +
149A ILE* 4.3 13.5 - - + -
271A PHE* 4.2 22.7 - - + -
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Residues in contact with GLY 95 (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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91A ASP 3.1 12.2 + - - -
92A LEU 3.3 4.0 + - - -
93A SER 3.2 0.2 - - - -
94A ALA* 1.3 73.6 - - - +
96A MET* 1.3 62.7 + - - +
98A LEU* 3.2 8.6 + - - +
99A VAL* 3.0 26.5 + - - +
263A ALA 6.0 0.2 - - - -
275A ALA* 3.1 30.5 - - - +
278A PRO* 3.7 8.1 - - - -
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Residues in contact with MET 96 (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 ALA* 3.2 16.6 - - - +
82A LEU* 3.9 22.7 - - + -
83A ALA* 4.2 11.0 - - + +
88A MET* 3.4 33.2 - - + -
92A LEU 3.1 8.5 + - - +
93A SER 3.1 8.8 + - - +
95A GLY* 1.3 70.5 - - - +
97A VAL* 1.3 68.6 + - - +
99A VAL* 3.2 7.7 + - - +
100A GLY 2.9 17.7 + - - -
219A VAL* 4.7 1.3 - - - -
222A ALA* 3.5 37.5 - - + +
223A VAL* 4.5 11.2 - - - +
226A HIS* 4.3 14.9 - - - +
278A PRO* 3.6 22.8 - - + +
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Residues in contact with VAL 97 (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 PRO* 5.0 1.7 - - - +
79A ALA* 3.9 6.7 - - - -
80A TRP* 4.3 19.5 - - + +
83A ALA* 5.6 1.6 - - + -
93A SER* 2.9 21.4 + - - +
94A ALA* 3.6 11.0 - - - +
96A MET* 1.3 73.7 - - - +
98A LEU* 1.3 58.1 + - - +
100A GLY* 3.1 2.6 + - - -
101A SER* 2.8 38.1 + - - +
141A THR* 3.7 40.4 - - + +
144A TYR* 3.6 38.4 - - + +
145A VAL* 4.6 1.1 - - + -
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Residues in contact with LEU 98 (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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94A ALA 2.9 13.9 + - - +
95A GLY* 3.5 10.1 - - - +
96A MET 3.2 0.4 - - - -
97A VAL* 1.3 76.6 - - - +
99A VAL* 1.3 63.4 + - - +
101A SER* 3.1 9.1 + - - +
102A VAL* 3.2 24.1 + - + +
137A THR* 4.1 11.0 - - + -
141A THR* 3.5 23.3 - - + +
156A MET* 4.1 19.3 - - - -
263A ALA* 3.7 12.1 - - - +
266A LEU* 3.7 15.5 - - + -
267A GLY* 3.3 39.0 - - - +
271A PHE* 3.8 20.0 - - + -
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Residues in contact with VAL 99 (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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95A GLY 3.0 15.6 + - - +
96A MET* 3.5 8.5 - - - +
98A LEU* 1.3 75.3 - - - +
100A GLY* 1.3 52.4 + - - +
101A SER 3.4 0.3 + - - -
102A VAL* 3.4 5.2 - - - +
223A VAL* 6.0 0.2 - - + -
226A HIS* 4.0 7.0 - - + +
258A GLN* 2.7 35.7 + - + +
260A SER* 4.8 2.2 - - - -
263A ALA* 3.7 14.3 - - + +
278A PRO* 3.7 8.7 - - + -
279A GLY* 3.4 35.2 - - - +
282A PHE* 3.4 43.3 - - + -
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Residues in contact with GLY 100 (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 HIS* 4.8 1.7 + - - +
72A TYR* 5.5 0.2 - - - -
75A MET* 3.3 40.7 - - - +
76A PRO* 3.3 12.2 - - - +
79A ALA* 4.0 1.8 - - - -
96A MET 2.9 12.8 + - - -
97A VAL 3.1 4.7 + - - -
99A VAL* 1.3 77.3 - - - +
101A SER* 1.3 59.0 + - - +
102A VAL 4.3 0.3 - - - +
226A HIS* 3.4 12.7 - - - -
258A GLN* 3.3 7.2 + - - -
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Residues in contact with SER 101 (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 TYR* 3.5 13.2 - - - -
76A PRO* 3.7 15.7 - - - +
97A VAL* 2.8 28.4 + - - +
98A LEU 3.1 2.8 + - - -
100A GLY* 1.3 76.9 - - - +
102A VAL* 1.3 58.8 + - - +
137A THR* 2.7 28.9 + - - -
140A LEU* 3.6 25.6 - - - +
141A THR* 3.8 17.4 + - - -
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Residues in contact with VAL 102 (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 HIS* 2.9 21.4 - - - -
72A TYR* 4.1 0.9 - - - -
98A LEU* 3.2 14.1 + - + +
99A VAL 3.4 18.8 - - - +
101A SER* 1.3 79.0 - - - +
103A ALA* 1.3 71.8 + - - +
137A THR* 3.4 19.5 - - + -
258A GLN* 3.2 8.2 + - + +
259A ASN* 3.5 29.4 - - + +
262A LEU* 4.5 14.6 - - + -
263A ALA* 3.9 26.9 - - + +
266A LEU* 4.6 3.6 - - + -
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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