Contacts of the helix formed by residues 93 - 106 (chain D) in PDB entry 3SPD
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 HIS 93 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80D HIS* 5.0 7.0 - + - -
81D LEU* 3.5 17.4 - - + +
84D VAL* 4.1 14.9 - - + +
88D GLU* 3.5 18.6 - - + +
89D ILE* 2.8 38.8 + - + +
92D LYS* 1.3 89.6 + - + +
94D ARG* 1.3 65.1 + - - +
96D LEU* 3.1 12.5 + - + +
97D VAL* 3.1 14.0 + - - +
703D SO4 2.7 38.0 + - - +
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Residues in contact with ARG 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90D MET* 2.8 55.5 + - - +
91D MET 4.4 11.4 - - - +
92D LYS 3.7 2.5 + - - -
93D HIS* 1.3 73.7 - - - +
95D SER* 1.3 60.6 + - - +
97D VAL* 3.7 28.0 - - - +
98D GLU* 2.9 49.9 + - - +
177D ILE 5.0 4.6 + - - -
178D ASP* 6.1 1.0 - - - +
179D THR 4.7 7.9 + - - -
180D PRO* 6.1 0.4 - - - +
181D THR* 3.9 14.6 + - - +
703D SO4 5.2 0.2 + - - -
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Residues in contact with SER 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D HIS 3.2 0.8 - - - -
94D ARG* 1.3 79.0 - - - +
96D LEU* 1.3 56.4 + - - +
98D GLU* 3.4 10.8 + - - +
99D LYS* 2.9 29.5 + - - +
703D SO4 3.4 23.6 + - - -
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Residues in contact with LEU 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D THR* 4.3 15.9 - - - +
81D LEU* 3.8 28.0 - - + -
89D ILE* 3.9 18.6 - - + -
93D HIS* 3.1 5.6 + - + +
95D SER* 1.3 74.3 - - - +
97D VAL* 1.3 65.8 + - - +
99D LYS* 3.1 20.4 + - + +
100D LEU* 2.9 50.4 + - + +
146D LEU* 3.9 27.8 - - + -
703D SO4 2.9 22.2 + - - +
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Residues in contact with VAL 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D ILE* 3.8 27.4 - - + +
90D MET* 4.2 9.6 - - - -
93D HIS 3.1 14.8 + - - +
94D ARG* 3.7 37.9 - - - +
95D SER 3.3 0.2 - - - -
96D LEU* 1.3 77.0 - - - +
98D GLU* 1.3 63.9 + - + +
100D LEU* 3.3 8.4 + - - +
101D VAL* 3.0 27.3 + - + +
137D PHE* 5.4 0.2 - - + -
177D ILE* 3.7 34.3 - - + +
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Residues in contact with GLU 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D ARG* 2.9 40.3 + - + +
95D SER* 3.8 9.1 + - - +
97D VAL* 1.3 79.2 - - + +
99D LYS* 1.3 56.9 + - - +
101D VAL* 3.4 7.5 + - - +
102D SER* 2.9 30.0 + - - -
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Residues in contact with LYS 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D ASP* 3.1 32.4 + - + +
58D VAL* 5.0 3.4 - - + -
95D SER 2.9 18.6 + - - +
96D LEU* 3.1 22.8 + - + +
98D GLU* 1.3 74.5 - - - +
100D LEU* 1.3 64.9 + - - +
102D SER* 3.3 7.8 + - - -
103D TYR* 3.0 51.7 + - + -
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Residues in contact with LEU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D VAL* 4.2 20.0 - - + -
74D LEU* 3.9 35.7 - - + +
76D THR* 5.0 6.7 - - - +
89D ILE* 5.5 0.9 - - + -
96D LEU* 2.9 46.5 + - + +
97D VAL* 3.8 7.6 - - - +
99D LYS* 1.3 73.2 - - + +
101D VAL* 1.3 67.6 + - + +
103D TYR* 3.2 5.7 + - - +
104D VAL* 3.0 26.4 + - - +
137D PHE* 4.1 27.1 - - + -
146D LEU* 5.1 3.4 - - + -
148D LEU* 4.2 17.7 - - + -
177D ILE* 5.1 2.2 - - + -
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Residues in contact with VAL 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D VAL* 3.0 26.1 + - + +
98D GLU* 3.8 7.0 - - - +
100D LEU* 1.3 74.4 - - - +
102D SER* 1.3 58.7 + - - +
104D VAL* 3.2 7.0 + - + +
105D GLN* 2.9 60.2 + - + +
135D VAL* 6.3 0.2 - - + -
148D LEU* 6.1 0.7 - - + -
177D ILE* 3.6 36.6 - - + +
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Residues in contact with SER 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D GLU 2.9 19.2 + - - -
99D LYS* 3.5 8.7 - - - -
100D LEU 3.2 0.2 - - - -
101D VAL* 1.3 78.4 - - - +
103D TYR* 1.3 57.1 + - - +
105D GLN* 3.9 3.3 - - - +
106D GLY* 3.0 28.8 + - - -
107D ASP 4.1 0.9 + - - -
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Residues in contact with TYR 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D TYR* 3.9 9.9 - + - -
55D ASP* 2.6 34.1 + - - -
57D ASP* 3.7 12.8 + - - +
58D VAL* 3.6 36.3 - - + -
74D LEU* 4.2 5.4 - - + -
99D LYS* 3.0 46.6 + - + -
100D LEU* 3.5 8.7 - - - +
102D SER* 1.3 76.4 - - - +
104D VAL* 1.3 60.8 + - - +
106D GLY 3.4 3.6 + - - -
107D ASP* 3.6 15.2 + - + +
108D LEU* 2.9 57.9 + - + +
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Residues in contact with VAL 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D LEU* 4.0 9.4 - - + -
100D LEU 3.0 17.2 + - - +
101D VAL* 3.2 9.6 + - - +
103D TYR* 1.3 75.7 - - - +
105D GLN* 1.3 68.5 + - + +
108D LEU* 4.6 0.7 - - + -
109D SER* 3.4 21.8 - - - -
112D ILE* 4.1 19.4 - - + +
133D ILE* 6.3 0.4 - - + -
135D VAL* 4.4 22.0 - - + -
148D LEU* 4.6 7.2 - - + -
150D ILE* 3.8 32.1 - - + -
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Residues in contact with GLN 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D VAL* 2.9 41.2 + - + +
102D SER* 3.9 3.0 - - - +
104D VAL* 1.3 84.5 - - + +
106D GLY* 1.3 58.6 + - - +
109D SER* 3.8 11.9 + - - -
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Residues in contact with GLY 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D SER 3.0 15.3 + - - -
104D VAL 3.3 1.6 - - - -
105D GLN* 1.3 77.5 - - - +
107D ASP* 1.3 63.2 + - - -
108D LEU 3.2 0.9 - - - -
109D SER* 2.7 29.3 + - - -
110D GLY 4.5 0.3 + - - -
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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