Contacts of the helix formed by residues 99 - 112 (chain A) in PDB entry 1LVK
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A ARG* 4.6 6.4 + - - +
45A ASP* 4.3 0.2 - - - +
47A TYR* 4.1 12.3 + - + +
78A ASN* 5.0 0.2 + - - -
98A ASN* 1.3 73.0 - - - +
100A PRO* 1.3 67.8 - - + +
102A VAL* 3.1 7.5 + - - +
103A PHE* 2.9 28.2 + - - +
673A LEU* 4.0 14.4 - - + +
677A ARG* 3.3 33.8 + - - +
682A LEU* 3.5 37.1 - - + +
686A ARG* 4.8 8.5 + - - -
689A ARG* 5.6 0.6 - - - +
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Residues in contact with PRO 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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36A TRP* 3.4 33.3 - - + -
47A TYR* 3.3 47.1 - - + +
78A ASN* 3.6 11.9 - - + +
98A ASN* 3.0 19.3 - - - +
99A GLU* 1.3 97.7 - - + +
101A ALA* 1.3 53.9 + - - -
103A PHE* 3.2 8.1 + - + +
104A HIS* 2.8 30.3 + - - +
673A LEU* 5.5 0.4 - - + -
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Residues in contact with ALA 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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36A TRP* 3.8 15.7 - - + +
79A GLN 4.5 1.6 - - - +
81A ASN* 3.9 13.3 + - - +
94A LEU* 4.4 5.0 - - + +
96A TYR 3.6 22.9 - - - +
98A ASN* 3.0 29.5 + - - +
99A GLU 3.1 0.2 - - - -
100A PRO* 1.3 75.4 - - - +
102A VAL* 1.3 64.3 + - - +
104A HIS* 3.3 6.8 + - - +
105A ASN* 3.1 21.5 + - - +
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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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91A MET* 3.6 29.1 - - + +
94A LEU* 4.5 12.6 - - + -
97A LEU* 4.3 14.4 - - + +
98A ASN 2.9 23.8 + - - +
99A GLU* 3.6 6.1 - - - +
101A ALA* 1.3 73.9 - - - +
103A PHE* 1.3 65.5 + - - +
105A ASN 3.2 1.7 + - - -
106A LEU* 3.2 18.4 + - + +
676A LEU* 4.9 10.5 - - + -
681A VAL* 5.1 4.0 - - + -
682A LEU* 4.3 13.7 - - + -
685A ILE* 3.9 33.2 - - + -
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Residues in contact with PHE 103 (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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45A ASP 5.6 0.2 - - - -
47A TYR* 6.3 2.0 - + - -
99A GLU 2.9 14.8 + - - +
100A PRO* 3.8 6.1 - - + +
102A VAL* 1.3 77.5 - - - +
104A HIS* 1.3 65.6 + - - +
106A LEU* 3.2 10.5 + - + +
107A ARG* 2.9 55.6 + - + +
667A LEU* 3.4 39.7 - - + -
669A ASP* 3.4 37.2 - - + -
672A VAL* 3.7 36.6 - - + -
673A LEU* 4.0 24.2 - - + +
676A LEU* 5.2 1.1 - - - -
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Residues in contact with HIS 104 (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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36A TRP* 3.5 36.8 - + + -
80A ARG* 3.6 13.4 + - + -
81A ASN* 6.3 1.6 - - + -
86A ASP* 2.9 41.7 + - - -
100A PRO 2.8 18.0 + - - +
101A ALA* 3.4 8.1 - - - +
103A PHE* 1.3 81.4 - - - +
105A ASN* 1.3 59.4 + - + +
107A ARG* 3.5 19.4 + - - +
108A VAL* 2.9 46.0 + - + +
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Residues in contact with ASN 105 (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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85A PHE 3.4 7.4 + - - -
86A ASP* 3.8 1.8 + - - +
87A GLY* 2.7 36.7 - - - +
88A VAL* 2.9 37.7 - - - +
91A MET* 3.6 28.5 - - - +
94A LEU* 4.3 8.7 - - + +
101A ALA 3.1 13.2 + - - +
102A VAL 3.2 1.3 + - - +
103A PHE 3.2 0.2 - - - -
104A HIS* 1.3 76.4 - - + +
106A LEU* 1.3 68.4 + - - +
108A VAL* 3.4 3.1 + - - +
109A ARG* 3.1 32.7 + - - +
117A THR* 3.9 2.3 - - - +
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Residues in contact with LEU 106 (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 MET* 3.4 23.7 - - + +
102A VAL* 3.2 8.8 + - + +
103A PHE* 3.2 11.6 + - + +
105A ASN* 1.3 83.5 - - - +
107A ARG* 1.3 52.5 + - - +
109A ARG* 3.4 5.4 + - - +
110A TYR* 2.8 34.1 + - - +
114A LEU 4.8 0.7 - - - +
117A THR* 3.7 22.2 - - - +
124A VAL* 4.2 17.3 - - + +
126A VAL* 4.2 21.7 - - + +
656A ILE* 5.7 0.9 - - + -
667A LEU* 4.7 4.0 - - + -
672A VAL* 4.3 14.1 - - + -
676A LEU* 4.1 31.2 - - + -
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Residues in contact with ARG 107 (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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36A TRP* 6.0 4.0 - - - -
47A TYR 5.6 4.4 + - - -
103A PHE* 2.9 48.4 + - + +
104A HIS* 3.5 20.1 + - - +
106A LEU* 1.3 75.3 - - - +
108A VAL* 1.4 58.0 + - - +
110A TYR* 3.6 0.4 - - - +
111A ASN* 2.8 55.9 + - - +
667A LEU* 3.6 33.8 + - + +
669A ASP* 4.6 10.5 + - - -
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Residues in contact with VAL 108 (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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86A ASP* 4.2 15.5 - - + +
87A GLY* 4.0 20.9 - - - +
104A HIS* 2.9 51.7 + - + +
105A ASN* 3.8 5.8 - - - +
107A ARG* 1.4 76.3 - - + +
109A ARG* 1.3 63.7 + - - +
111A ASN* 3.4 20.9 + - - +
112A GLN* 3.0 33.4 + - - +
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Residues in contact with ARG 109 (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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15A LEU 4.5 8.1 + - - -
17A VAL* 4.1 5.3 - - - +
87A GLY* 3.0 31.5 + - - -
88A VAL 3.2 20.4 + - - -
89A GLU* 3.6 21.7 + - - +
105A ASN* 3.1 22.0 + - - +
106A LEU 3.6 3.4 - - - +
108A VAL* 1.3 75.1 - - - +
110A TYR* 1.3 56.8 + - - +
112A GLN* 2.9 14.0 + - - +
114A LEU* 2.9 68.4 + - + +
116A TYR 2.7 22.4 + - - -
117A THR* 3.0 23.6 + - - +
153A PRO* 3.7 18.4 + - - +
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Residues in contact with TYR 110 (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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106A LEU* 2.8 20.2 + - + +
107A ARG* 3.6 9.6 - - - +
109A ARG* 1.3 73.2 - - - +
111A ASN* 1.3 59.6 + - - +
112A GLN 3.0 0.2 - - - -
113A ASP* 2.8 27.1 + - - +
114A LEU 3.6 7.4 + - - +
115A ILE* 4.2 13.2 - - + -
126A VAL* 3.4 39.7 - - + -
127A ASN 2.7 24.3 + - - -
128A PRO* 3.5 19.4 + - + +
658A PRO* 3.4 16.5 - - + +
663A LEU 4.7 0.7 + - - -
665A ALA* 4.4 14.4 + - - -
666A LYS 4.4 13.7 - - - -
667A LEU* 3.8 31.4 - - + -
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Residues in contact with ASN 111 (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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107A ARG* 2.8 43.8 + - - +
108A VAL* 3.5 13.0 - - - +
109A ARG 3.1 0.2 - - - -
110A TYR* 1.3 80.7 - - - +
112A GLN* 1.3 62.1 + - + +
113A ASP* 3.3 2.7 + - - +
667A LEU* 6.0 1.2 - - - +
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Residues in contact with GLN 112 (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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13A LYS 5.2 4.7 - - - +
14A TYR* 5.3 1.0 - - - +
16A LYS 5.9 0.4 - - - +
17A VAL* 3.9 37.1 - - - +
18A LYS* 4.6 3.3 + - - +
108A VAL* 3.0 37.6 + - - +
109A ARG* 2.9 8.6 + - - +
111A ASN* 1.3 82.0 - - + +
113A ASP* 1.3 72.2 + - - +
114A LEU* 3.1 18.7 + - + +
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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