Contacts of the helix formed by residues 108 - 123 (chain S) in PDB entry 3SDI
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 ALA 108 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
761 GLU* 3.8 28.0 - - + +
74S MET* 3.9 1.1 - - - +
106S LYS 3.5 4.4 + - - -
107S LEU* 1.3 79.1 - - - +
109S VAL* 1.3 65.7 + - - +
110S GLU* 4.3 6.3 - - + +
111S ARG* 3.0 21.7 + - + +
112S ALA 3.0 18.0 + - - -
142S ASP* 3.6 11.4 - - - +
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Residues in contact with VAL 109 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73S HIS* 5.2 1.1 - - - +
74S MET* 3.7 15.7 - - + -
107S LEU 3.5 0.8 + - - +
108S ALA* 1.3 67.9 - - - +
110S GLU* 1.3 66.5 + - - +
112S ALA* 3.1 5.2 + - - +
113S GLY 2.9 18.7 + - - -
138S ILE* 4.1 21.8 - - + +
139S ILE 4.9 0.2 - - - -
140S GLY* 3.8 29.4 - - - +
141S TYR 5.2 0.2 - - - -
142S ASP* 3.0 21.7 + - + +
147S HIS* 3.9 29.6 - - + -
149S LEU* 3.4 24.5 - - + +
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Residues in contact with GLU 110 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681 ASP 2.9 26.2 - - - +
691 ASN* 4.3 0.7 - - - +
701 PRO* 3.3 27.1 - - - +
108S ALA* 4.3 6.0 - - + +
109S VAL* 1.3 78.2 - - - +
111S ARG* 1.3 57.3 + - - +
113S GLY* 3.0 4.4 + - - +
114S HIS* 2.9 52.0 + - + +
142S ASP* 4.8 0.6 + - - -
147S HIS* 5.6 6.2 + - + -
149S LEU* 4.8 8.9 - - - +
159S GLU* 4.5 13.1 - - - +
63T LYS* 4.5 19.6 - - - +
65T VAL* 6.1 1.1 - - - +
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Residues in contact with ARG 111 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641 GLU* 5.9 5.3 + - - +
671 TYR 5.4 7.9 + - - -
681 ASP* 5.8 3.6 - - - -
691 ASN* 6.5 0.7 - - - -
99S SER* 5.6 0.6 + - - -
107S LEU* 3.8 26.0 - - + +
108S ALA* 3.0 24.8 + - + +
110S GLU* 1.3 77.1 - - - +
112S ALA* 1.3 62.3 + - - +
114S HIS* 3.4 16.1 + - - +
115S LEU* 3.1 48.4 + - + +
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Residues in contact with ALA 112 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74S MET* 3.6 29.8 - - + -
92S LEU* 3.7 25.5 - - + +
107S LEU* 4.4 4.3 - - + +
108S ALA 3.0 5.9 + - - -
109S VAL* 3.2 9.4 - - - +
111S ARG* 1.3 72.4 - - - +
113S GLY* 1.3 64.3 + - - +
115S LEU* 3.1 9.7 + - - +
116S LEU* 3.0 29.5 + - + +
138S ILE* 5.2 6.1 - - + -
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Residues in contact with GLY 113 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109S VAL 2.9 11.3 + - - -
110S GLU* 3.0 5.3 + - - -
112S ALA* 1.3 77.2 - - - +
114S HIS* 1.3 62.7 + - - +
115S LEU 3.1 0.3 + - - -
116S LEU* 3.3 5.6 + - - +
117S CYS* 3.0 24.0 + - - +
138S ILE* 5.5 0.2 - - - -
149S LEU* 3.9 19.7 - - - +
157S VAL* 3.7 20.4 - - - +
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Residues in contact with HIS 114 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681 ASP* 3.7 27.0 + - + +
110S GLU* 2.9 56.1 + - + +
111S ARG* 3.8 16.8 - - + +
112S ALA 3.4 0.2 - - - -
113S GLY* 1.3 76.1 - - - +
115S LEU* 1.3 58.1 + - + +
117S CYS* 3.6 4.0 + - - +
118S ASP* 3.1 34.7 + - - +
65T VAL 5.6 5.2 - - - -
86T ARG* 3.1 41.1 + - - +
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Residues in contact with LEU 115 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91S TYR* 3.7 33.6 + - + +
92S LEU* 5.3 2.2 - - + -
95S GLN* 3.9 35.2 - - + +
107S LEU* 4.2 11.9 - - + -
111S ARG* 3.1 48.3 + - + +
112S ALA* 3.1 8.8 + - - +
114S HIS* 1.3 76.8 - - + +
116S LEU* 1.3 60.5 + - - +
118S ASP* 3.3 8.4 + - + +
119S LYS* 3.0 27.5 + - - +
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Residues in contact with LEU 116 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76S LEU* 5.3 0.4 - - + -
88S LEU* 3.9 45.5 - - + +
91S TYR* 4.4 12.1 - - + -
92S LEU* 4.3 21.3 - - + -
112S ALA 3.0 18.6 + - - +
113S GLY* 3.7 4.5 - - - +
115S LEU* 1.3 73.7 - - - +
117S CYS* 1.3 67.5 + - - +
119S LYS* 3.0 3.8 + - - +
120S ALA* 2.9 25.3 + - - +
136S LEU* 4.3 14.8 - - + -
138S ILE* 3.4 32.3 - - + -
151S PHE* 3.7 18.7 - - + -
157S VAL* 6.0 0.2 - - + -
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Residues in contact with CYS 117 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113S GLY 3.0 16.7 + - - +
114S HIS* 3.7 7.0 - - - +
116S LEU* 1.3 75.2 - - - +
118S ASP* 1.3 70.0 + - - +
120S ALA* 3.3 2.3 + - - +
121S GLN* 2.8 27.4 + - - +
151S PHE* 4.2 1.2 - - - -
155S GLY* 2.9 35.0 - - - +
157S VAL* 4.1 11.2 - - + +
82T ILE* 5.8 1.6 - - - -
83T PRO* 4.2 17.5 - - - -
86T ARG* 3.7 20.9 - - - +
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Residues in contact with ASP 118 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91S TYR* 6.0 0.4 - - - +
114S HIS 3.1 15.5 + - - +
115S LEU* 3.7 7.9 - - + +
116S LEU 3.2 0.4 - - - -
117S CYS* 1.3 79.4 - - - +
119S LYS* 1.3 62.6 + - - +
121S GLN* 3.5 8.6 + - - +
122S LYS* 3.4 39.4 + - - +
83T PRO 5.3 0.7 - - - +
86T ARG* 3.0 41.6 + - - +
87T HIS* 4.9 2.3 + - - -
90T ASN* 2.7 28.5 + - - +
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Residues in contact with LYS 119 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87S VAL* 4.6 11.7 - - - +
88S LEU* 3.8 18.8 - - + -
91S TYR* 3.7 51.1 + - + -
115S LEU 3.0 14.0 + - - +
116S LEU* 3.0 8.7 + - - +
118S ASP* 1.3 77.7 - - - +
120S ALA* 1.3 62.0 + - - +
122S LYS* 3.6 14.4 + - + +
123S ASN* 3.5 21.7 + - - +
132S TYR* 3.3 26.7 + - - +
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Residues in contact with ALA 120 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88S LEU* 5.2 0.4 - - - +
116S LEU 2.9 14.9 + - - +
117S CYS 3.7 3.4 - - - +
119S LYS* 1.3 76.2 - - - +
121S GLN* 1.3 64.3 + - - +
123S ASN* 3.3 14.4 + - - +
124S THR* 3.3 16.9 + - - +
131S PRO* 5.5 0.2 - - - +
132S TYR* 3.9 15.8 - - + -
151S PHE* 3.6 28.0 - - + -
153S PRO 3.8 10.6 - - - +
155S GLY* 3.7 12.8 - - - -
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Residues in contact with GLN 121 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117S CYS* 2.8 17.6 + - - +
118S ASP* 3.7 10.2 + - - +
119S LYS 3.3 0.4 - - - -
120S ALA* 1.3 76.5 - - - +
122S LYS* 1.3 74.9 + - - +
124S THR* 2.8 28.8 + - - +
125S GLN* 2.7 29.0 + - - +
154S SER 5.0 0.4 - - - -
155S GLY* 4.7 0.6 - - - -
83T PRO* 3.4 40.8 - - + +
84T ASP* 3.2 16.2 - - - +
87T HIS* 3.1 36.4 + - + +
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Residues in contact with LYS 122 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118S ASP* 3.4 26.7 + - - +
119S LYS* 4.0 10.6 - - + +
120S ALA 3.3 0.8 - - - -
121S GLN* 1.3 89.6 - - - +
123S ASN* 1.3 60.5 + - - +
125S GLN* 3.1 19.4 + - - +
126S SER* 3.5 15.9 + - - -
87T HIS* 4.7 19.5 - - + +
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Residues in contact with ASN 123 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12S THR* 4.1 5.2 + - - -
119S LYS* 3.5 9.9 + - - +
120S ALA 3.3 9.6 + - - +
121S GLN 3.2 0.6 - - - -
122S LYS* 1.3 80.0 - - - +
124S THR* 1.3 57.4 + - - +
125S GLN 3.4 2.0 + - - -
126S SER 4.8 4.0 + - - +
129S GLY* 4.5 8.0 - - - -
130S ARG* 3.3 34.8 + - - +
131S PRO* 3.5 20.4 - - + +
132S TYR* 2.9 44.0 + - + -
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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
------------------------------------------------------------
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