Contacts of the helix formed by residues 108 - 118 (chain A) in PDB entry 5XMA
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 GLU 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A ARG* 3.0 39.8 + - - -
104A ALA* 3.6 8.3 - - + +
105A LEU* 2.8 43.5 + - + +
107A GLU* 1.3 82.5 - - + +
109A LYS* 1.3 52.9 + - - +
110A PRO* 3.5 2.0 - - - -
111A TYR* 3.2 4.4 + - - -
112A ALA* 2.7 35.4 + - - +
139A GLN 3.7 4.2 - - - +
140A TYR* 3.5 38.8 - - + +
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Residues in contact with LYS 109 (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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32A LYS* 5.1 16.8 + - - +
35A VAL* 5.3 6.7 - - - +
55A ILE* 3.7 36.6 - - + +
104A ALA* 5.2 0.4 - - - -
105A LEU 3.1 5.2 + - - -
106A ALA* 3.5 15.7 - - - +
107A GLU 3.3 0.2 - - - -
108A GLU* 1.3 74.5 - - - +
110A PRO* 1.3 67.7 - - + +
112A ALA* 3.2 3.2 + - - +
113A ILE* 2.8 57.6 + - + +
154A THR* 5.2 6.3 - - + +
155A THR* 6.5 1.1 - - - +
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Residues in contact with PRO 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 ALA 4.8 1.3 - - - +
107A GLU 3.8 9.9 - - - +
108A GLU 3.6 1.8 - - - -
109A LYS* 1.3 97.1 - - + +
111A TYR* 1.3 70.4 + - + +
113A ILE* 3.7 4.8 + - + +
114A PHE* 3.4 23.0 + - - +
153A ILE* 3.6 22.4 - - + +
154A THR* 3.4 26.0 - - - +
155A THR 3.7 20.0 - - - +
156A GLU* 3.8 11.4 - - - +
159A LEU* 3.9 8.0 - - + +
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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
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107A GLU 4.2 13.2 - - - -
108A GLU 3.2 2.3 + - - +
110A PRO* 1.3 93.0 - - + +
112A ALA* 1.3 62.5 + - - +
114A PHE* 3.8 4.3 + - - +
115A HIS* 3.5 14.4 + - - +
137A LEU* 4.9 7.5 - - + +
138A ASN 4.0 4.8 - - - +
139A GLN* 3.1 16.7 - - - +
140A TYR 3.3 29.2 - - - +
141A GLY* 3.5 17.7 - - - +
142A LEU* 3.8 22.7 - - + -
148A LEU* 5.6 2.9 - - + +
149A VAL 3.7 16.9 + - - -
150A PRO* 4.7 1.2 - - - +
151A LEU* 4.0 22.5 + - - +
153A ILE* 4.5 6.2 - - + +
159A LEU* 3.7 33.3 - - + +
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Residues in contact with ALA 112 (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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53A LEU* 3.6 20.6 - - + -
104A ALA* 3.8 18.6 - - + -
108A GLU* 2.7 22.6 + - + +
109A LYS* 3.7 2.2 - - - +
111A TYR* 1.3 71.9 - - - +
113A ILE* 1.3 66.8 + - - +
115A HIS* 3.0 12.5 + - - +
116A PHE* 3.1 20.8 + - + -
139A GLN* 2.9 20.6 + - + +
140A TYR* 6.4 0.2 - - + -
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Residues in contact with ILE 113 (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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35A VAL* 4.8 23.1 - - + -
37A VAL* 4.3 6.8 - - + +
41A ARG* 4.0 25.8 - - - +
53A LEU* 4.2 15.7 - - + -
55A ILE* 5.8 0.7 - - + -
109A LYS* 2.8 53.9 + - + +
110A PRO* 4.0 7.2 - - + +
111A TYR 3.6 0.2 - - - -
112A ALA* 1.3 71.5 - - - +
114A PHE* 1.3 60.1 + - - +
116A PHE 3.5 0.5 + - - -
117A THR* 2.6 33.8 + - - +
155A THR* 6.5 0.2 - - - -
156A GLU* 4.1 20.4 - - + +
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Residues in contact with PHE 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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110A PRO 3.4 15.1 + - - +
111A TYR 4.0 4.9 - - - +
112A ALA 3.2 0.4 - - - -
113A ILE* 1.3 79.8 - - - +
115A HIS* 1.3 68.0 + - - +
117A THR* 3.4 11.1 + - - -
118A GLY 3.8 3.7 + - - +
122A TYR* 3.9 33.9 - + - -
123A LEU* 3.9 24.6 - - + +
126A ILE* 4.7 16.2 - - + -
127A ARG* 5.8 1.1 - - - -
137A LEU* 4.0 30.7 - - + -
156A GLU* 3.5 27.4 - - + +
159A LEU* 4.9 9.0 - - + -
160A ILE* 4.2 24.7 - - + -
163A LEU* 5.2 11.7 - - + -
173A ARG* 4.1 5.8 + - - -
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Residues in contact with HIS 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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111A TYR 3.5 3.7 + - - +
112A ALA 3.0 7.7 + - - +
114A PHE* 1.3 84.2 - - + +
116A PHE* 1.3 100.5 + + - +
117A THR 3.1 0.5 + - - -
118A GLY 3.2 8.8 + - - -
123A LEU* 3.5 15.9 - - - +
127A ARG* 2.9 29.4 + - - +
139A GLN* 3.5 38.4 + - + -
2E G 4.1 12.9 + - - -
22F C 4.9 0.8 + - - -
23F A 3.1 49.4 + + - +
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Residues in contact with PHE 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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37A VAL* 3.7 24.2 - - + -
38A GLY 3.1 14.0 + - - -
53A LEU* 3.9 30.1 - - + -
102A PHE* 3.4 46.4 - + + -
103A THR 5.5 2.9 - - - -
104A ALA* 5.9 0.2 - - + -
112A ALA* 3.1 23.3 + - + +
115A HIS* 1.3 102.1 - + - +
117A THR* 1.3 59.1 + - - +
118A GLY 3.3 0.2 - - - -
139A GLN* 4.2 21.1 - - + -
22F C 5.1 4.5 - - - -
23F A 2.8 37.0 - - - +
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Residues in contact with THR 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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37A VAL* 3.9 4.2 - - - +
38A GLY 3.8 7.9 - - - +
41A ARG* 2.7 51.9 + - + +
42A ARG* 2.7 33.1 + - + +
113A ILE 2.6 23.4 + - - -
114A PHE 3.7 6.1 - - - -
115A HIS 3.1 1.0 + - - -
116A PHE* 1.3 77.6 - - - +
118A GLY* 1.3 59.6 + - - +
170A PRO* 4.2 15.3 - - + -
173A ARG* 3.6 15.2 + - - +
23F A 3.5 0.6 - - - +
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Residues in contact with GLY 118 (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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42A ARG* 3.6 3.7 - - - -
114A PHE* 3.8 3.9 + - - +
115A HIS 3.2 7.5 + - - -
116A PHE 3.3 0.4 - - - -
117A THR* 1.3 88.5 - - - +
119A PRO* 1.3 76.2 - - - +
122A TYR* 4.1 4.9 - - - -
123A LEU* 3.7 17.6 - - - +
173A ARG* 4.0 14.7 + - - +
23F A 3.7 5.6 - - - -
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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