Contacts of the helix formed by residues 93 - 110 (chain A) in PDB entry 1LD8
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 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ILE 3.8 1.2 + - - -
92A TYR* 1.3 78.3 - - - +
94A ASP* 1.3 64.9 + - - +
95A LYS* 3.7 7.5 + - - +
96A PHE* 3.1 23.7 + - - +
97A ARG* 3.1 19.6 + - - +
126A LEU* 5.4 1.6 - - - +
591B ASP* 4.2 13.8 - - - +
594B GLU* 2.8 17.0 + - - -
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Residues in contact with ASP 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LEU* 3.4 11.6 - - - +
67A ARG* 2.8 42.2 + - - -
92A TYR 3.9 0.4 + - - -
93A SER* 1.3 72.1 - - - +
95A LYS* 1.3 59.0 + - + +
97A ARG* 3.5 16.0 + - - +
98A ASP* 3.0 28.6 + - - +
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Residues in contact with LYS 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 2.8 37.8 + - + +
59A ASP* 4.7 6.7 + - - +
63A TYR* 3.8 24.8 + - + -
65A LEU* 3.6 24.0 - - + -
93A SER* 3.3 7.0 + - - +
94A ASP* 1.3 80.0 - - + +
96A PHE* 1.3 61.3 + - - +
98A ASP* 3.6 1.2 - - - +
99A VAL* 3.2 29.5 + - - +
126A LEU* 4.5 5.4 - - + -
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Residues in contact with PHE 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A TYR* 3.3 33.2 - + - -
93A SER* 3.1 14.5 + - - +
95A LYS* 1.3 79.0 - - - +
97A ARG* 1.3 65.5 + - - +
99A VAL* 3.3 0.9 + - - +
100A TYR* 3.1 48.3 + + + -
126A LEU* 3.7 48.8 - - + +
127A ASN* 4.2 3.1 - - + -
594B GLU* 3.2 52.9 - - + +
597B ASP* 3.7 27.1 - - + -
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Residues in contact with ARG 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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90A ILE 5.3 0.2 + - - -
91A ILE* 4.7 5.7 - - - +
92A TYR* 3.3 52.1 + - + +
93A SER 3.1 10.4 + - - +
94A ASP* 4.0 17.1 + - - +
96A PHE* 1.3 84.9 - - - +
98A ASP* 1.3 57.3 + - - +
100A TYR* 3.3 3.4 + - - -
101A ASP* 2.8 58.2 + - - +
104A ARG* 4.9 4.5 - - - +
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Residues in contact with ASP 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A TYR* 4.3 3.3 + - - -
65A LEU* 3.5 18.6 - - + +
66A TYR* 2.7 35.4 + - - +
67A ARG* 3.1 43.6 + - - +
94A ASP 3.0 19.6 + - - +
95A LYS 3.6 4.9 - - - +
96A PHE 3.2 0.2 - - - -
97A ARG* 1.3 79.8 - - - +
99A VAL* 1.3 62.8 + - - +
101A ASP* 3.3 4.5 + - - +
102A TYR* 3.2 30.9 + - - -
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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
----------------------------------------------------------
58A LEU* 4.4 1.6 - - + -
63A TYR* 3.4 26.2 - - - +
66A TYR* 3.9 13.7 - - + -
95A LYS 3.2 11.6 + - - +
98A ASP* 1.3 80.5 - - - +
100A TYR* 1.3 60.8 + - + +
102A TYR* 3.3 4.9 + - - +
103A PHE* 2.8 23.9 + - - +
119A LEU* 3.8 17.8 - - + +
122A ASP* 4.1 6.5 - - + -
123A ALA* 3.7 38.6 - - + +
126A LEU* 3.5 22.2 - - + -
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Residues in contact with TYR 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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96A PHE* 3.1 52.7 + + + +
97A ARG* 4.1 1.6 - - - +
99A VAL* 1.3 80.5 - - + +
101A ASP* 1.3 60.7 + - - +
103A PHE* 3.6 16.7 - + + +
104A ARG* 2.9 60.8 + - - +
123A ALA* 2.8 41.7 + - + +
126A LEU* 4.1 10.1 - - + -
127A ASN* 3.8 5.8 - - + +
130A ASN* 3.4 39.4 - - - +
133A VAL* 3.9 12.8 - - + +
597B ASP* 4.8 5.8 - - - -
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Residues in contact with ASP 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PRO* 3.8 19.9 - - + +
78A VAL 2.8 31.2 + - - +
79A PRO* 3.6 25.4 - - - +
80A GLN 4.0 0.7 + - - -
97A ARG* 2.8 44.4 + - - +
98A ASP* 3.7 6.6 + - - +
99A VAL 3.3 0.2 - - - -
100A TYR* 1.3 72.3 - - - +
102A TYR* 1.3 62.7 + - + +
104A ARG* 2.8 20.7 + - - +
105A ALA 3.3 8.3 + - - -
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Residues in contact with TYR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A TYR* 3.6 22.3 + - + -
67A ARG* 3.3 42.3 + - + +
72A TRP* 3.7 35.7 + + + -
73A ALA* 5.9 0.5 - - - -
75A ILE* 3.7 25.6 + - + -
77A PRO* 3.6 36.4 - - + +
98A ASP* 3.2 23.9 + - - +
99A VAL 3.3 7.2 + - - +
100A TYR 3.2 0.4 - - - -
101A ASP* 1.3 77.8 - - + +
103A PHE* 1.3 64.9 + - - +
104A ARG 3.2 0.4 - - - -
105A ALA* 3.1 5.7 + - + +
106A VAL* 3.0 23.7 + - - +
119A LEU* 3.8 15.1 - - + +
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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
----------------------------------------------------------
99A VAL 2.8 17.7 + - - +
100A TYR* 3.8 21.5 - + + +
102A TYR* 1.3 76.0 - - - +
104A ARG* 1.3 65.4 + - + +
106A VAL* 2.9 30.7 - - + +
107A LEU* 2.9 36.7 + - + +
119A LEU* 3.7 10.9 - - + +
120A THR* 4.4 10.1 - - + -
123A ALA* 4.8 8.1 - - + -
130A ASN* 5.1 1.1 - - - -
132A THR* 4.1 16.4 - - + -
133A VAL* 3.6 52.7 - - + -
136A PHE* 4.0 25.1 - + + -
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Residues in contact with ARG 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A VAL* 3.0 37.9 + - + +
79A PRO 4.2 2.0 - - - -
80A GLN* 3.5 48.0 + - - +
92A TYR* 6.0 2.6 - - - -
97A ARG* 4.2 6.1 + - - +
100A TYR* 2.9 47.5 + - - +
101A ASP* 2.8 23.0 + - - +
102A TYR 3.2 0.2 - - - -
103A PHE* 1.3 86.1 - - + +
105A ALA* 1.3 56.2 + - - +
107A LEU* 3.9 7.3 - - + +
108A GLN* 3.0 32.2 + - - +
597B ASP* 5.3 2.2 + - - -
644B PRO 5.0 9.7 + - - +
645B GLY* 6.2 3.1 - - - -
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Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ILE* 3.8 16.6 - - + +
76A ASP 3.3 26.9 - - - +
77A PRO* 4.2 1.1 - - + -
78A VAL* 3.6 14.1 - - + +
101A ASP 3.3 11.2 + - - +
102A TYR* 3.1 14.6 + - + +
104A ARG* 1.3 78.6 - - - +
106A VAL* 1.3 60.1 + - - +
108A GLN* 3.9 2.4 + - - +
109A ARG* 3.0 30.3 + - - +
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Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TRP* 5.0 6.5 - - + -
75A ILE* 4.2 4.9 - - + +
102A TYR 3.0 12.8 + - - +
103A PHE* 2.9 34.3 - - + +
105A ALA* 1.3 73.5 - - - +
107A LEU* 1.3 55.6 + - - +
109A ARG* 3.3 4.4 + - - -
110A ASP* 2.7 29.5 + - - -
111A GLU* 3.0 39.6 + - + +
116A ALA* 3.3 32.8 - - + +
119A LEU* 4.1 11.7 - - + -
120A THR* 6.2 0.2 - - + -
136A PHE* 3.8 14.2 - - + -
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Residues in contact with LEU 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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103A PHE* 2.9 33.6 + - + +
104A ARG* 3.9 7.9 - - + +
106A VAL* 1.3 78.5 - - + +
108A GLN* 1.3 59.1 + - - +
110A ASP* 2.9 20.8 + - - +
132A THR* 3.8 24.2 - - + -
136A PHE* 3.6 31.6 - - + -
645B GLY 4.2 15.5 - - - +
647B TYR* 3.1 33.4 - - + +
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Residues in contact with GLN 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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78A VAL* 3.8 32.2 - - - +
104A ARG 3.0 19.7 + - - +
105A ALA 3.9 3.3 + - - +
107A LEU* 1.3 77.8 - - - +
109A ARG* 1.3 58.7 + - - +
110A ASP* 3.7 1.4 + - - +
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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
----------------------------------------------------------
74A ASP* 3.9 10.3 + - - -
75A ILE* 3.5 34.2 - - + +
105A ALA 3.0 17.9 + - - +
106A VAL* 3.8 4.0 - - - +
108A GLN* 1.3 76.1 - - - +
110A ASP* 1.3 72.4 + - - +
111A GLU* 3.1 30.7 + - + +
115A ARG* 3.6 10.9 - - - +
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Residues in contact with ASP 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 VAL 2.7 9.3 + - - -
107A LEU 2.9 12.3 + - - +
108A GLN 4.9 1.3 - - - +
109A ARG* 1.3 81.2 - - - +
111A GLU* 1.3 60.5 + - - +
112A ARG* 2.8 47.5 + - - +
136A PHE* 3.9 13.6 - - - -
139A VAL* 5.2 0.7 - - - +
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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
------------------------------------------------------------
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