Contacts of the helix formed by residues 99 - 116 (chain B) in PDB entry 3DDN
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 ASN 99 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B VAL* 3.5 28.9 - - + +
96B PRO 4.6 2.9 - - - +
97B THR 4.4 1.8 - - - -
98B SER* 1.3 78.1 + - - +
100B ILE* 1.3 68.1 + - + +
101B HIS 3.3 1.8 + - - -
102B SER* 3.3 5.5 + - - -
103B ALA* 2.9 31.0 + - - +
153B ILE* 3.4 23.3 - - + +
283B ALA* 3.3 18.6 - - - +
288B ALA* 4.9 4.3 - - - -
600B HPV 3.0 27.1 + - - +
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Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B PRO 5.1 1.1 - - - +
97B THR* 3.4 39.9 + - + +
98B SER 3.4 1.0 - - - -
99B ASN* 1.3 79.8 - - + +
101B HIS* 1.3 89.9 + - + +
104B ALA* 3.1 26.3 + - - +
152B ARG* 4.5 25.1 - - + +
153B ILE* 3.9 23.3 - - + +
156B LEU* 4.1 19.5 - - + +
322B GLU* 6.1 0.2 - - - -
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Residues in contact with HIS 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLU* 3.7 21.7 + - - +
141A PHE* 3.5 61.8 - + + -
98B SER 5.2 0.8 + - - -
100B ILE* 1.3 92.8 - - + +
102B SER* 1.3 59.3 + - - +
104B ALA* 3.3 4.3 + - - +
105B GLU* 2.9 40.7 + - - +
156B LEU* 3.8 24.8 - - + +
160B ARG* 3.9 10.6 + - - +
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Residues in contact with SER 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ARG* 3.0 20.9 + - - +
139A GLU* 2.5 25.3 + - - +
99B ASN 3.3 6.0 + - - -
101B HIS* 1.3 78.7 - - - +
103B ALA* 1.3 56.7 + - - +
105B GLU* 3.5 2.6 + - - -
106B HIS* 3.0 22.5 + - - +
282B GLY 3.2 16.3 - - - +
283B ALA* 4.3 2.5 - - - -
285B THR* 2.7 30.7 + - - +
288B ALA* 4.1 10.1 - - - -
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ASN* 2.9 26.6 + - - +
102B SER* 1.3 72.7 - - - +
104B ALA* 1.3 60.7 + - - +
106B HIS* 3.3 3.4 + - - +
107B ALA* 3.0 27.4 + - - +
153B ILE* 3.7 30.0 - - + +
231B ALA* 4.9 11.8 - - - +
282B GLY* 3.3 15.4 + - - +
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ILE 3.1 19.5 + - - +
101B HIS* 3.7 4.0 - - - +
103B ALA* 1.3 73.6 - - - +
105B GLU* 1.3 66.7 + - - +
107B ALA* 3.2 5.2 + - - +
108B LEU* 3.1 27.2 + - - +
153B ILE* 3.9 6.3 - - + +
156B LEU* 4.0 25.8 - - + -
157B VAL* 3.8 18.4 - - + -
160B ARG* 4.4 14.1 - - - +
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Residues in contact with GLU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A LEU* 3.9 11.6 - - + +
116A ARG* 4.0 10.7 + - - +
138A THR 4.3 0.9 - - - +
139A GLU* 3.4 15.4 - - - +
140A ILE* 2.8 32.8 + - + +
141A PHE* 3.0 31.4 + - - +
164A PHE* 3.6 32.8 - - + +
101B HIS* 2.9 23.0 + - - +
102B SER 3.8 3.6 - - - +
104B ALA* 1.3 76.3 - - - +
106B HIS* 1.3 52.4 + - - +
108B LEU* 3.1 3.8 + - - +
109B ALA* 2.7 35.7 + - - +
160B ARG* 4.9 5.3 + - - +
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Residues in contact with HIS 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ARG* 3.7 27.4 - - + +
118A ILE* 3.8 26.5 - - + -
102B SER 3.0 18.9 + - - +
103B ALA 3.7 4.3 - - - +
104B ALA 3.2 0.4 - - - -
105B GLU* 1.3 72.1 - - - +
107B ALA* 1.3 66.5 + - - +
109B ALA* 3.6 3.8 - - - +
110B LEU* 3.0 38.1 + - + +
231B ALA* 4.5 3.1 - - + -
257B ASP* 3.3 31.9 + - + -
278B THR* 2.9 28.7 + - + -
281B LEU* 4.2 12.2 - - + +
282B GLY* 3.7 12.8 - - - -
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ALA 3.0 14.2 + - - +
104B ALA 3.4 9.4 - - - +
106B HIS* 1.3 77.9 - - - +
108B LEU* 1.3 62.0 + - + +
110B LEU* 3.4 2.4 + - - +
111B LEU* 3.1 23.3 + - - +
157B VAL* 3.8 19.3 - - + -
201B SER* 4.3 8.7 + - - +
203B HIS* 3.9 16.6 - - + -
229B VAL* 3.9 8.7 - - + +
231B ALA* 4.3 16.3 - - + +
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A LEU* 4.2 4.5 - - + -
164A PHE* 3.7 25.8 - - + -
104B ALA 3.1 18.5 + - - +
105B GLU 3.4 7.6 - - - +
107B ALA* 1.3 75.4 - - - +
109B ALA* 1.3 65.5 + - - +
111B LEU* 3.3 9.4 + - + +
112B LEU* 3.0 31.3 + - + +
140B ILE* 6.0 0.2 - - + -
157B VAL* 3.8 29.6 - - + +
160B ARG* 4.1 16.8 - - + -
161B ILE* 3.9 27.4 - - + -
164B PHE* 4.0 25.4 - - + -
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ALA 5.5 1.7 - - - +
112A LEU* 3.6 40.5 - - + +
113A ALA* 5.6 1.0 + - - -
116A ARG* 4.6 3.8 - - + -
118A ILE* 4.6 9.6 - - + +
105B GLU 2.7 20.4 + - - +
106B HIS* 3.3 18.8 + - - +
108B LEU* 1.3 72.5 - - - +
110B LEU* 1.3 58.0 + - - +
112B LEU* 3.4 2.2 + - - +
113B ALA* 2.9 30.0 + - - +
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ILE* 4.9 4.7 - - + -
106B HIS* 3.0 30.7 + - + +
107B ALA 3.8 3.6 - - - +
108B LEU 3.2 0.2 - - - -
109B ALA* 1.3 73.7 - - - +
111B LEU* 1.3 61.7 + - - +
113B ALA* 3.9 2.4 - - - +
114B ALA* 2.8 33.6 + - - +
229B VAL* 4.1 10.5 - - + -
231B ALA* 3.9 11.4 - - + -
255B GLY* 4.3 6.8 - - - +
256B LEU* 4.0 14.6 - - - +
257B ASP* 3.8 37.5 - - + +
276B VAL* 4.1 25.3 - - + +
278B THR* 4.0 20.9 - - + +
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B ALA 3.1 17.3 + - - +
108B LEU* 3.6 9.0 - - + +
110B LEU* 1.3 78.4 - - - +
112B LEU* 1.3 61.5 + - + +
114B ALA* 3.9 2.8 - - - +
115B SER* 2.8 37.7 + - - +
140B ILE* 3.6 32.5 - - + -
145B VAL* 5.0 4.3 - - + -
157B VAL* 6.2 1.3 - - + -
161B ILE* 4.3 24.5 - - + -
199B PHE* 4.1 31.6 - - + -
200B ILE 5.5 2.0 - - - +
201B SER* 5.2 9.9 - - - +
227B ILE* 4.8 1.6 - - + +
229B VAL* 3.6 22.6 - - + +
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Residues in contact with LEU 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A GLU* 3.7 24.5 - - + +
108A LEU 4.3 0.4 - - - -
109A ALA* 3.7 27.6 - - + +
112A LEU* 3.6 24.2 - - + -
108B LEU* 3.0 24.9 + - + +
109B ALA* 3.9 2.9 - - - +
111B LEU* 1.3 78.7 - - + +
113B ALA* 1.3 59.2 + - - +
115B SER* 3.2 5.1 + - - -
116B ARG* 2.9 38.6 + - + +
140B ILE* 3.5 30.3 - - + -
164B PHE* 4.1 23.6 - - + -
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Residues in contact with ALA 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ALA* 5.1 0.8 + - - +
113A ALA* 5.3 3.1 - - + -
118A ILE* 3.8 30.5 - - + -
109B ALA 2.9 18.7 + - - +
110B LEU* 3.9 4.5 - - - +
112B LEU* 1.3 78.1 - - - +
114B ALA* 1.3 56.2 + - - +
117B GLN* 2.9 24.8 + - - -
118B ILE* 3.0 23.7 + - + -
119B PRO* 4.1 7.9 - - + -
276B VAL* 3.7 10.3 - - + +
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Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LEU 2.8 17.5 + - - +
111B LEU* 4.0 3.8 - - - +
113B ALA* 1.3 76.4 - - - +
115B SER* 1.3 63.8 + - - +
116B ARG 3.6 0.2 + - - -
117B GLN* 3.8 10.8 + - - +
227B ILE* 4.2 11.3 - - + +
229B VAL* 5.2 0.2 - - + -
253B ALA* 3.5 18.1 - - - +
254B ALA 3.7 37.5 - - - +
255B GLY* 4.2 1.1 - - - +
274B GLN 4.8 0.7 - - - +
276B VAL* 3.8 11.4 - - + +
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Residues in contact with SER 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B LEU* 2.8 24.6 + - - +
112B LEU* 3.2 9.6 + - - -
114B ALA* 1.3 79.5 - - - +
116B ARG* 1.3 62.0 + - - +
117B GLN* 4.3 3.0 - - - +
136B SER 4.7 0.2 - - - +
137B GLY* 3.2 6.2 - - - -
138B THR* 3.1 40.5 + - - +
140B ILE* 4.9 3.7 - - - +
199B PHE* 3.1 29.0 - - - -
227B ILE* 3.7 12.1 - - - +
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Residues in contact with ARG 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A SER* 2.8 30.5 + - - +
105A GLU* 4.0 11.7 + - - +
106A HIS* 3.6 27.6 + - + +
109A ALA* 4.4 8.7 - - + -
281A LEU* 3.0 35.6 + - + +
282A GLY 2.8 28.9 + - - -
284A SER 4.3 2.4 + - - +
285A THR* 3.9 13.8 + - - -
112B LEU* 2.9 20.7 + - + +
115B SER* 1.3 85.7 - - - +
117B GLN* 1.3 76.0 + - - +
118B ILE* 3.0 22.5 + - + +
135B PHE* 5.5 0.2 - - - +
137B GLY* 4.2 11.5 - - - -
138B THR 4.0 14.1 + - - -
139B GLU* 5.4 0.2 - - - +
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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
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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