Contacts of the strand formed by residues 104 - 117 (chain A) in PDB entry 2HUE
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 ARG 104 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A HIS* 5.7 0.4 + - - -
100A SER* 3.3 2.6 - - - -
101A TYR* 2.7 50.6 + - - +
102A ASP* 2.8 45.0 + - - +
103A GLY* 1.3 73.0 - - - +
105A GLU* 1.3 65.1 + - - +
106A PHE 3.4 1.2 + - - -
151A ILE* 3.8 24.8 - - + +
152A VAL* 2.7 38.3 + - - +
153A TRP 4.1 4.8 + - - -
155A ASN* 3.8 24.6 + - - +
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Residues in contact with GLU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A SER* 3.9 9.8 - - - -
99A CYS 3.6 13.2 - - - +
100A SER* 3.9 7.6 - - - -
103A GLY 3.9 2.8 + - - -
104A ARG* 1.3 70.5 - - - +
106A PHE* 1.3 61.7 + - - +
107A VAL 4.1 5.2 - - - +
108A ARG* 2.7 52.6 + - - +
149A PHE* 3.6 34.8 - - + +
151A ILE* 3.3 14.0 - - - +
132B GLY 5.0 1.4 - - - +
134B ARG* 6.0 2.1 - - - +
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Residues in contact with PHE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SER* 5.8 1.6 - - - +
4A VAL* 3.5 42.0 - - + -
5A SER* 5.0 2.9 - - - -
6A LEU 5.3 0.9 - - - -
38A LEU* 3.7 8.3 - - + -
40A TRP* 5.1 1.8 - + - -
99A CYS* 3.0 46.6 + - + -
100A SER 3.6 11.2 - - - -
101A TYR* 3.8 12.3 - - + -
104A ARG 3.9 1.6 - - - -
105A GLU* 1.3 75.2 - - - +
107A VAL* 1.3 80.5 + - + +
148A ARG* 3.5 6.8 + - - +
149A PHE* 2.9 41.2 + - - +
151A ILE* 3.9 16.4 - - + -
153A TRP* 3.6 22.7 - + + -
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 4.5 23.1 - - + +
40A TRP* 4.6 12.3 - - + -
97A LEU 4.8 0.7 - - - +
98A SER* 3.4 3.0 - - - -
99A CYS* 2.9 42.9 + - + +
105A GLU* 3.8 5.0 - - - +
106A PHE* 1.3 104.4 - - + +
108A ARG* 1.3 67.2 + - - +
109A VAL* 4.5 0.9 - - + -
146A VAL* 3.9 23.8 - - + -
147A THR 3.2 12.3 - - - +
148A ARG* 4.1 10.3 - - + +
149A PHE* 4.6 0.7 - - - -
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Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU* 4.0 33.7 - - + +
97A LEU 3.7 4.9 - - - +
98A SER* 4.2 14.1 + - - +
105A GLU* 2.7 39.2 + - - +
107A VAL* 1.3 73.2 - - - +
109A VAL* 1.3 72.7 + - - +
110A GLY 4.9 0.4 - - - +
145A ARG 3.7 1.2 - - - +
146A VAL* 3.5 2.3 - - - -
147A THR* 2.8 37.9 + - - +
149A PHE* 4.4 4.7 - - + -
129B ARG* 4.4 8.8 + - - +
130B ILE 5.3 1.6 - - - +
132B GLY* 3.2 46.2 + - - +
133B GLU* 3.9 14.6 + - - +
134B ARG 5.2 0.4 - - - +
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Residues in contact with VAL 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.5 32.3 - - + -
9A ILE* 3.9 14.6 - - + -
40A TRP* 6.2 0.9 - - + -
95A ILE 3.8 0.3 - - - +
96A LEU* 3.3 2.8 - - - +
97A LEU* 2.7 49.6 + - + +
107A VAL* 4.5 2.9 - - + -
108A ARG* 1.3 81.9 - - - +
110A GLY* 1.3 61.1 + - - +
111A TYR* 3.7 27.9 + - + -
144A PRO* 3.9 21.8 - - + -
145A ARG 3.4 3.1 - - - +
146A VAL* 4.1 12.6 - - + -
100C PHE* 4.1 3.6 - - + -
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Residues in contact with GLY 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE 3.4 7.9 - - - -
96A LEU* 4.0 7.9 - - - -
108A ARG* 4.2 0.4 - - - +
109A VAL* 1.3 74.6 - - - +
111A TYR* 1.3 60.5 + - - -
144A PRO* 3.6 4.7 - - - +
145A ARG 2.8 35.4 + - - -
130B ILE* 3.4 29.7 + - - +
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Residues in contact with TYR 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 3.5 35.2 + - + +
11A VAL* 4.0 11.4 - - + +
24A PHE* 4.1 15.7 - + - -
94A VAL* 3.2 5.7 - - - +
95A ILE* 3.0 54.3 + - + -
97A LEU* 4.7 5.2 - - + -
109A VAL* 3.7 17.7 - - + +
110A GLY* 1.3 75.2 - - - -
112A TYR* 1.3 62.4 + - - +
113A VAL* 3.9 0.2 - - - +
139A ILE* 3.7 24.5 - - + -
140A LEU 3.5 19.1 - - - +
141A ALA* 3.9 19.4 + - - -
143A LYS 5.1 1.3 - - - -
144A PRO* 3.6 32.3 - - + +
130B ILE* 3.8 6.0 - - - +
100C PHE* 4.2 1.9 - - - -
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Residues in contact with TYR 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A VAL* 4.6 2.5 - - + -
93A THR 3.5 3.8 - - - -
94A VAL* 3.5 26.7 - - + -
111A TYR* 1.3 75.1 - - - +
113A VAL* 1.3 59.1 + - - +
139A ILE* 3.5 3.5 - - - +
140A LEU* 2.8 51.6 + - + +
143A LYS 5.5 2.2 + - - -
145A ARG* 5.0 0.9 - - + -
106B ASP* 2.7 32.3 + - - -
109B LEU* 3.9 14.4 - - + -
110B CYS* 3.4 42.3 - - + +
113B HIS* 3.9 20.0 - - + -
126B LEU* 4.3 3.6 - - + -
127B ALA* 3.5 8.7 - - - -
130B ILE* 3.2 40.5 - - + +
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TYR* 4.7 4.7 - - + +
44A TYR* 5.0 3.1 - - + -
91A SER 4.1 1.0 - - - +
92A VAL* 3.2 3.8 - - - -
93A THR* 2.8 46.8 + - + +
94A VAL 4.5 0.2 - - - -
95A ILE* 3.7 41.5 - - + +
111A TYR 3.9 2.9 - - - +
112A TYR* 1.3 79.0 - - - +
114A ASN* 1.3 71.8 + - - +
115A ASN* 3.9 8.7 + - - +
137A ARG* 4.0 23.3 - - + -
138A ASN 3.5 6.5 - - - +
139A ILE* 4.0 18.6 - - + -
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Residues in contact with ASN 114 (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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92A VAL* 3.8 9.1 + - + +
113A VAL* 1.3 74.4 - - - +
115A ASN* 1.3 64.6 + - - +
116A GLU* 4.2 10.2 + - - +
136A VAL 3.8 0.6 - - - +
137A ARG* 3.2 5.0 - - - +
138A ASN* 2.8 39.5 + - + +
501A GOL 2.9 50.2 + - - -
113B HIS* 3.4 40.3 + - + +
114B ALA* 3.7 4.7 - - - -
115B LYS* 4.4 7.9 - - - +
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Residues in contact with ASN 115 (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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18A PHE* 3.7 15.4 - - - -
44A TYR* 3.2 23.5 + - - -
89A LEU 3.6 18.4 + - - +
90A VAL* 3.5 8.5 - - - -
91A SER 3.0 26.6 + - - +
93A THR* 4.2 3.2 - - - +
113A VAL* 4.1 8.3 + - - +
114A ASN* 1.3 78.4 + - - +
116A GLU* 1.3 60.5 + - - +
135A ILE* 3.8 12.6 - - + +
136A VAL 3.4 3.4 - - - -
137A ARG* 3.4 24.0 - - - +
501A GOL 2.9 24.7 + - - -
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Residues in contact with GLU 116 (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 VAL* 4.0 5.2 - - - -
114A ASN* 4.2 5.4 - - - +
115A ASN* 1.3 75.6 - - - +
117A TYR* 1.3 70.7 + - - +
123A ARG* 3.6 33.8 + - + -
135A ILE* 4.1 1.9 - - - +
136A VAL* 2.8 36.8 + - + +
501A GOL 2.7 35.8 + - - +
115B LYS* 2.9 30.6 + - - +
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Residues in contact with TYR 117 (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 VAL* 3.8 23.9 - - + +
116A GLU* 1.3 81.4 - - - +
118A ASP* 1.3 58.5 + - - +
119A GLU 3.3 2.2 - - - +
122A LEU* 3.6 37.5 - - + -
123A ARG* 3.1 35.3 + - + +
126A PRO* 4.1 13.7 - - + -
127A PRO* 4.0 26.9 + - + +
130A VAL* 3.4 16.1 - - - +
131A GLN* 3.0 47.3 + - + -
134A HIS* 3.3 22.7 - - + -
135A ILE* 3.8 12.1 - - + -
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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